From af48cede1fa9a287a78e13ec2d00c1ae4a00cc89 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Mon, 27 Feb 2023 09:58:28 +0100
Subject: [PATCH 01/41] Update protocol repository default view styles
 [SCI-7996]

---
 app/assets/stylesheets/extend/datatable.scss               | 2 +-
 app/assets/stylesheets/partials/_sidebar.scss              | 5 +++--
 app/assets/stylesheets/shared/content_pane.scss            | 2 +-
 app/assets/stylesheets/shared_styles/elements/buttons.scss | 4 ++++
 app/views/protocols/index/_general_toolbar.html.erb        | 2 +-
 config/locales/en.yml                                      | 2 +-
 6 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/app/assets/stylesheets/extend/datatable.scss b/app/assets/stylesheets/extend/datatable.scss
index 8e5fa96d8..5fdc55233 100644
--- a/app/assets/stylesheets/extend/datatable.scss
+++ b/app/assets/stylesheets/extend/datatable.scss
@@ -54,7 +54,7 @@
     }
 
     td {
-      padding-left: 10px;
+      padding: 14px 8px;
 
       .nowrap {
         white-space: nowrap;
diff --git a/app/assets/stylesheets/partials/_sidebar.scss b/app/assets/stylesheets/partials/_sidebar.scss
index bc180e478..2ac4e8e3d 100644
--- a/app/assets/stylesheets/partials/_sidebar.scss
+++ b/app/assets/stylesheets/partials/_sidebar.scss
@@ -149,7 +149,7 @@
       margin-left: -2.5em;
       max-width: var(--wrapper-width);
       overflow: hidden;
-      padding: 1em 2.5em;
+      padding: 1em;
       text-decoration: none;
       text-overflow: ellipsis;
       white-space: nowrap;
@@ -162,7 +162,8 @@
       &.selected {
         background: $color-white;
         color: $brand-primary;
-        font-weight: bold;
+        font-weight: normal;
+        padding-left: 2.5em;
       }
 
       .fas {
diff --git a/app/assets/stylesheets/shared/content_pane.scss b/app/assets/stylesheets/shared/content_pane.scss
index c0914267b..6c4aa3400 100644
--- a/app/assets/stylesheets/shared/content_pane.scss
+++ b/app/assets/stylesheets/shared/content_pane.scss
@@ -9,7 +9,7 @@
 
   &.flexible {
     margin: 0;
-    padding: 0 1em;
+    padding: 0 9px;
   }
 
   .content-header {
diff --git a/app/assets/stylesheets/shared_styles/elements/buttons.scss b/app/assets/stylesheets/shared_styles/elements/buttons.scss
index 608087c51..fb31a9346 100644
--- a/app/assets/stylesheets/shared_styles/elements/buttons.scss
+++ b/app/assets/stylesheets/shared_styles/elements/buttons.scss
@@ -233,6 +233,10 @@
     float: left;
     margin: 2px 4px 2px 0;
 
+    .fas {
+      margin-right: 8px;
+    }
+
     &:nth-last-child(1) {
       margin-right: 0;
     }
diff --git a/app/views/protocols/index/_general_toolbar.html.erb b/app/views/protocols/index/_general_toolbar.html.erb
index 1e41b9c3c..17d331f92 100644
--- a/app/views/protocols/index/_general_toolbar.html.erb
+++ b/app/views/protocols/index/_general_toolbar.html.erb
@@ -14,7 +14,7 @@
         data-toggle="dropdown"
         aria-haspopup="true"
         aria-expanded="false">
-        <span class="fas fa-download"></span><span class="hidden-xs"><%= t("protocols.index.import") %></span>
+        <span class="fas fa-upload"></span><span class="hidden-xs"><%= t("protocols.index.import") %></span>
       </button>
       <% if can_create_protocols_in_repository?(@current_team) %>
         <ul class="dropdown-menu">
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 6ed5c4562..e1bc72a21 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -313,7 +313,7 @@ en:
     templates:
       sidebar_title: "TEMPLATES"
       protocol_templates: "Protocol templates"
-      label_templates: "Label Templates"
+      label_templates: "Label templates"
 
   nav2:
     all_projects:

From e02705c3f1a01f3abca1158f513a25273a9dc727 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Mon, 27 Feb 2023 16:07:46 +0100
Subject: [PATCH 02/41] Update actions toolbar styles [SCI-7996]

---
 app/assets/stylesheets/protocols/index.scss  |  1 +
 app/assets/stylesheets/shared/datatable.scss | 28 ++++++++++++++++----
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/app/assets/stylesheets/protocols/index.scss b/app/assets/stylesheets/protocols/index.scss
index eaf29b46f..23e346339 100644
--- a/app/assets/stylesheets/protocols/index.scss
+++ b/app/assets/stylesheets/protocols/index.scss
@@ -46,6 +46,7 @@
       flex-direction: column;
       flex-grow: 1;
       height: calc(100% - var(--datatable-pagination-row) - var(--protocol-toolbar-size));
+      padding-bottom: 12px;
     }
 
     .dataTables_scrollBody {
diff --git a/app/assets/stylesheets/shared/datatable.scss b/app/assets/stylesheets/shared/datatable.scss
index 6b5ea33c4..c641c5bcc 100644
--- a/app/assets/stylesheets/shared/datatable.scss
+++ b/app/assets/stylesheets/shared/datatable.scss
@@ -39,8 +39,10 @@
   .pagination-row {
     align-items: center;
     display: flex;
+    align-items: center;
     flex-wrap: wrap;
-    min-height: var(--datatable-pagination-row);
+    height: var(--datatable-pagination-row);
+    box-shadow: inset 0px 1px 0px $color-concrete;
     position: relative;
     width: 100%;
 
@@ -48,16 +50,34 @@
       align-items: center;
       background-color: $color-concrete;
       border-bottom: 1px solid $color-alto;
+      box-shadow: 0px -12px 24px -12px rgba(35, 31, 32, 0.2);
+      border-radius: 6px 6px 0px 0px;
       display: none;
       height: 70px;
       overflow-x: auto;
       padding: 0 1em;
       position: absolute;
-      top: 0;
+      bottom: var(--datatable-pagination-row);
       width: 100%;
+      z-index: 10;
 
       .btn {
-        margin-right: .25em;
+        margin-right: .5em;
+
+        &:focus {
+          box-shadow: 0 0 0 4px rgba(96, 159, 255, .5);
+        }
+
+        &:not(.btn-primary) {
+          &:hover {
+            background-color: $color-white;
+          }
+
+          &:active {
+            outline-color: transparent;
+            background-color: $color-alto;
+          }
+        }
       }
     }
 
@@ -127,10 +147,8 @@
   }
 
   &.show-actions {
-    --datatable-pagination-row: 139px;
 
     .pagination-row {
-      padding-top: 71px;
 
       .actions-toolbar {
         display: flex;

From 65c7a9fa9520c110cbe776f02a3c33d8d2d0177c Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Mon, 27 Feb 2023 17:10:20 +0100
Subject: [PATCH 03/41] Fix the rest of styles [SCI-7996]

---
 app/assets/stylesheets/partials/_sidebar.scss      |  3 +--
 app/assets/stylesheets/shared/content_pane.scss    |  2 +-
 app/assets/stylesheets/shared/datatable.scss       |  2 +-
 app/assets/stylesheets/shared/filter_dropdown.scss | 12 ++++++++++++
 4 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/app/assets/stylesheets/partials/_sidebar.scss b/app/assets/stylesheets/partials/_sidebar.scss
index 2ac4e8e3d..df7e0d640 100644
--- a/app/assets/stylesheets/partials/_sidebar.scss
+++ b/app/assets/stylesheets/partials/_sidebar.scss
@@ -149,7 +149,7 @@
       margin-left: -2.5em;
       max-width: var(--wrapper-width);
       overflow: hidden;
-      padding: 1em;
+      padding: 1em 2.5em;
       text-decoration: none;
       text-overflow: ellipsis;
       white-space: nowrap;
@@ -163,7 +163,6 @@
         background: $color-white;
         color: $brand-primary;
         font-weight: normal;
-        padding-left: 2.5em;
       }
 
       .fas {
diff --git a/app/assets/stylesheets/shared/content_pane.scss b/app/assets/stylesheets/shared/content_pane.scss
index 6c4aa3400..c0914267b 100644
--- a/app/assets/stylesheets/shared/content_pane.scss
+++ b/app/assets/stylesheets/shared/content_pane.scss
@@ -9,7 +9,7 @@
 
   &.flexible {
     margin: 0;
-    padding: 0 9px;
+    padding: 0 1em;
   }
 
   .content-header {
diff --git a/app/assets/stylesheets/shared/datatable.scss b/app/assets/stylesheets/shared/datatable.scss
index c641c5bcc..8ca2d98fd 100644
--- a/app/assets/stylesheets/shared/datatable.scss
+++ b/app/assets/stylesheets/shared/datatable.scss
@@ -65,7 +65,7 @@
         margin-right: .5em;
 
         &:focus {
-          box-shadow: 0 0 0 4px rgba(96, 159, 255, .5);
+          box-shadow: 0 0 0 4px $brand-focus;
         }
 
         &:not(.btn-primary) {
diff --git a/app/assets/stylesheets/shared/filter_dropdown.scss b/app/assets/stylesheets/shared/filter_dropdown.scss
index 6840c6f9c..87ac1417e 100644
--- a/app/assets/stylesheets/shared/filter_dropdown.scss
+++ b/app/assets/stylesheets/shared/filter_dropdown.scss
@@ -29,12 +29,24 @@
       position: relative;
       width: 100%;
 
+      &.folders {
+        display: flex;
+        align-items: center;
+        column-gap: 8px;
+      }
+
       label {
         @include font-small;
         font-weight: bold;
         margin-bottom: .3em;
         user-select: none;
       }
+
+      .input-field:focus-within,
+      .datetime-picker-container:focus-within {
+        border: 1px solid $brand-focus;
+        border-radius: 4px;
+      }
     }
 
     .text-search-filter {

From 944e7123be1f9233a8730566fe3ce4653c06a384 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Mon, 27 Feb 2023 17:15:32 +0100
Subject: [PATCH 04/41] Fix hound [SCI-7996]

---
 app/assets/stylesheets/shared/datatable.scss       | 3 +--
 app/assets/stylesheets/shared/filter_dropdown.scss | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/app/assets/stylesheets/shared/datatable.scss b/app/assets/stylesheets/shared/datatable.scss
index 8ca2d98fd..0df994162 100644
--- a/app/assets/stylesheets/shared/datatable.scss
+++ b/app/assets/stylesheets/shared/datatable.scss
@@ -39,10 +39,9 @@
   .pagination-row {
     align-items: center;
     display: flex;
-    align-items: center;
     flex-wrap: wrap;
     height: var(--datatable-pagination-row);
-    box-shadow: inset 0px 1px 0px $color-concrete;
+    box-shadow: inset 0 1px 0 $color-concrete;
     position: relative;
     width: 100%;
 
diff --git a/app/assets/stylesheets/shared/filter_dropdown.scss b/app/assets/stylesheets/shared/filter_dropdown.scss
index 87ac1417e..bde531fb9 100644
--- a/app/assets/stylesheets/shared/filter_dropdown.scss
+++ b/app/assets/stylesheets/shared/filter_dropdown.scss
@@ -30,9 +30,9 @@
       width: 100%;
 
       &.folders {
-        display: flex;
         align-items: center;
         column-gap: 8px;
+        display: flex;
       }
 
       label {

From e6c92fc32802368d50dbf417be55236b2f8516e5 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Tue, 28 Feb 2023 14:53:53 +0100
Subject: [PATCH 05/41] Change only datatable styles related to protocol
 [SCI-7996]

---
 app/assets/stylesheets/extend/datatable.scss | 2 +-
 app/assets/stylesheets/protocols/index.scss  | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/app/assets/stylesheets/extend/datatable.scss b/app/assets/stylesheets/extend/datatable.scss
index 5fdc55233..8e5fa96d8 100644
--- a/app/assets/stylesheets/extend/datatable.scss
+++ b/app/assets/stylesheets/extend/datatable.scss
@@ -54,7 +54,7 @@
     }
 
     td {
-      padding: 14px 8px;
+      padding-left: 10px;
 
       .nowrap {
         white-space: nowrap;
diff --git a/app/assets/stylesheets/protocols/index.scss b/app/assets/stylesheets/protocols/index.scss
index 23e346339..e40b7d1e7 100644
--- a/app/assets/stylesheets/protocols/index.scss
+++ b/app/assets/stylesheets/protocols/index.scss
@@ -51,6 +51,10 @@
 
     .dataTables_scrollBody {
       height: 100%;
+
+      td:not(:first-child) {
+        padding: 14px 8px;
+      }
     }
 
     // Cells

From b6ddb79183f9383fa4c027270fb34ddb4ad37d74 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Tue, 28 Feb 2023 15:47:06 +0100
Subject: [PATCH 06/41] Change the action-toolbar behavior after input from
 product team [SCI-7996]

---
 app/assets/stylesheets/shared/datatable.scss | 27 ++++----------------
 1 file changed, 5 insertions(+), 22 deletions(-)

diff --git a/app/assets/stylesheets/shared/datatable.scss b/app/assets/stylesheets/shared/datatable.scss
index 0df994162..6b5ea33c4 100644
--- a/app/assets/stylesheets/shared/datatable.scss
+++ b/app/assets/stylesheets/shared/datatable.scss
@@ -40,8 +40,7 @@
     align-items: center;
     display: flex;
     flex-wrap: wrap;
-    height: var(--datatable-pagination-row);
-    box-shadow: inset 0 1px 0 $color-concrete;
+    min-height: var(--datatable-pagination-row);
     position: relative;
     width: 100%;
 
@@ -49,34 +48,16 @@
       align-items: center;
       background-color: $color-concrete;
       border-bottom: 1px solid $color-alto;
-      box-shadow: 0px -12px 24px -12px rgba(35, 31, 32, 0.2);
-      border-radius: 6px 6px 0px 0px;
       display: none;
       height: 70px;
       overflow-x: auto;
       padding: 0 1em;
       position: absolute;
-      bottom: var(--datatable-pagination-row);
+      top: 0;
       width: 100%;
-      z-index: 10;
 
       .btn {
-        margin-right: .5em;
-
-        &:focus {
-          box-shadow: 0 0 0 4px $brand-focus;
-        }
-
-        &:not(.btn-primary) {
-          &:hover {
-            background-color: $color-white;
-          }
-
-          &:active {
-            outline-color: transparent;
-            background-color: $color-alto;
-          }
-        }
+        margin-right: .25em;
       }
     }
 
@@ -146,8 +127,10 @@
   }
 
   &.show-actions {
+    --datatable-pagination-row: 139px;
 
     .pagination-row {
+      padding-top: 71px;
 
       .actions-toolbar {
         display: flex;

From 88610d6b38de43807eafb333dae7fc10158beee7 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Tue, 28 Feb 2023 16:11:11 +0100
Subject: [PATCH 07/41] Add a small code refactor [SCI-7996]

---
 app/assets/stylesheets/protocols/index.scss          | 12 ++++++++++++
 app/assets/stylesheets/shared/filter_dropdown.scss   | 12 ------------
 app/views/protocols/index/_protocol_filters.html.erb |  2 +-
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/app/assets/stylesheets/protocols/index.scss b/app/assets/stylesheets/protocols/index.scss
index e40b7d1e7..893ff3eeb 100644
--- a/app/assets/stylesheets/protocols/index.scss
+++ b/app/assets/stylesheets/protocols/index.scss
@@ -128,6 +128,18 @@
         width: 32px;
       }
     }
+
+    .select-block.has-draft {
+      align-items: center;
+      column-gap: 8px;
+      display: flex;
+    }
+
+    .input-field:focus-within,
+    .datetime-picker-container:focus-within {
+      border: 1px solid $brand-focus;
+      border-radius: 4px;
+    }
   }
 
   &.archived {
diff --git a/app/assets/stylesheets/shared/filter_dropdown.scss b/app/assets/stylesheets/shared/filter_dropdown.scss
index bde531fb9..6840c6f9c 100644
--- a/app/assets/stylesheets/shared/filter_dropdown.scss
+++ b/app/assets/stylesheets/shared/filter_dropdown.scss
@@ -29,24 +29,12 @@
       position: relative;
       width: 100%;
 
-      &.folders {
-        align-items: center;
-        column-gap: 8px;
-        display: flex;
-      }
-
       label {
         @include font-small;
         font-weight: bold;
         margin-bottom: .3em;
         user-select: none;
       }
-
-      .input-field:focus-within,
-      .datetime-picker-container:focus-within {
-        border: 1px solid $brand-focus;
-        border-radius: 4px;
-      }
     }
 
     .text-search-filter {
diff --git a/app/views/protocols/index/_protocol_filters.html.erb b/app/views/protocols/index/_protocol_filters.html.erb
index 4ba0db4e2..038798781 100644
--- a/app/views/protocols/index/_protocol_filters.html.erb
+++ b/app/views/protocols/index/_protocol_filters.html.erb
@@ -22,7 +22,7 @@
               data-placeholder="Select who has access">
       </select>
     </div>
-    <div class="select-block folders">
+    <div class="select-block has-draft">
       <span class="sci-checkbox-container">
         <%= check_box_tag :has_draft, 'accepted', false, {class: "sci-checkbox"} %>
         <span class="sci-checkbox-label"></span>

From 8460fe3693c7d9e5a97371fc3233afa799bf959d Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 08:58:41 +0100
Subject: [PATCH 08/41] Implement the grant access to all team members
 functionality [SCI-8032]

---
 .../javascripts/protocols/protocolsio.js      | 57 +++++++++++++++++--
 .../protocol_importers/_import_form.html.erb  |  2 +
 .../_preview_modal_footer.html.erb            | 28 ++++++++-
 3 files changed, 78 insertions(+), 9 deletions(-)

diff --git a/app/assets/javascripts/protocols/protocolsio.js b/app/assets/javascripts/protocols/protocolsio.js
index a0eaae4f8..c03ae7238 100644
--- a/app/assets/javascripts/protocols/protocolsio.js
+++ b/app/assets/javascripts/protocols/protocolsio.js
@@ -1,5 +1,5 @@
 /* global animateSpinner PerfectSb initHandsOnTable */
-/* global HelperModule */
+/* global HelperModule dropdownSelector */
 /* eslint-disable no-use-before-define, no-alert */
 
 function applyClickCallbackOnProtocolCards() {
@@ -194,6 +194,16 @@ function handleFormSubmit(modal) {
     e.preventDefault(); // avoid to execute the actual submit of the form.
     e.stopPropagation();
     animateSpinner(modal, true);
+
+    const visibility = $('#protocol-preview-modal .modal-footer #visibility').prop('checked');
+    const defaultPublicUserRoleId = $('#protocol-preview-modal .modal-footer #default_public_user_role_id')
+      .prop('value');
+    const visibilityField = $('#protocol-preview-modal #protocol_visibility');
+    const defaultPublicUserRoleIdField = $('#protocol-preview-modal #protocol_default_public_user_role_id');
+
+    visibilityField.prop('value', visibility ? 'visible' : 'hidden');
+    defaultPublicUserRoleIdField.prop('value', defaultPublicUserRoleId);
+
     $.ajax({
       type: 'POST',
       url: url,
@@ -215,7 +225,7 @@ function handleFormSubmit(modal) {
 
 function initLoadProtocolModalPreview() {
   $('.convert-protocol').off('click').on('click', function(e) {
-    var link = $('.full-preview-panel');
+    const link = $('.full-preview-panel');
     animateSpinner(null, true);
     $.ajax({
       url: link.data('url'),
@@ -226,10 +236,11 @@ function initLoadProtocolModalPreview() {
       },
       dataType: 'json',
       success: function(data) {
-        var modal = $('#protocol-preview-modal');
-        var modalTitle = modal.find('.modal-title');
-        var modalBody = modal.find('.modal-body');
-        var modalFooter = modal.find('.modal-footer');
+        $('#protocolsioModal').modal('hide');
+        const modal = $('#protocol-preview-modal');
+        const modalTitle = modal.find('.modal-title');
+        const modalBody = modal.find('.modal-body');
+        const modalFooter = modal.find('.modal-footer');
 
         modalTitle.html(data.title);
         modalBody.html(data.html);
@@ -243,6 +254,7 @@ function initLoadProtocolModalPreview() {
           showFormErrors(modal, data.validation_errors);
         }
 
+        initProtocolModalPreview();
         initFormSubmits();
         handleFormSubmit(modal);
       },
@@ -272,3 +284,36 @@ applySearchCallback();
 
 // Trigger initial retrieval of latest publications
 $('form.protocols-search-bar').submit();
+
+function initProtocolModalPreview() {
+  $('#protocol-preview-modal').on('change', '#visibility', function() {
+    const checkbox = this;
+    $('#protocol-preview-modal #roleSelectWrapper').toggleClass('hidden', !checkbox.checked);
+  });
+
+
+  const roleSelector = '#protocol-preview-modal #role_selector';
+
+  dropdownSelector.init(roleSelector, {
+    noEmptyOption: true,
+    singleSelect: true,
+    closeOnSelect: true,
+    selectAppearance: 'simple',
+    onChange: function() {
+      $('#protocol-preview-modal #default_public_user_role_id').val(dropdownSelector.getValues(roleSelector));
+    }
+  });
+
+  $('#protocol-preview-modal')
+    .on('ajax:error', 'form', function(e, error) {
+      let msg = error.responseJSON.error;
+      $('#protocol-preview-modal #protocol_name').parent().addClass('error').attr('data-error-text', msg);
+    })
+    .on('ajax:success', 'form', function(e, data) {
+      if (data.message) {
+        HelperModule.flashAlertMsg(data.message, 'success');
+      }
+      $('#protocol-preview-modal #protocol_name').parent().removeClass('error');
+      $('#protocol-preview-modal').modal('hide');
+    });
+}
diff --git a/app/views/protocol_importers/_import_form.html.erb b/app/views/protocol_importers/_import_form.html.erb
index 60c1ba35f..81786f747 100644
--- a/app/views/protocol_importers/_import_form.html.erb
+++ b/app/views/protocol_importers/_import_form.html.erb
@@ -32,6 +32,8 @@
   <%= f.hidden_field(:published_on, value: protocol.published_on) %>
   <%= f.hidden_field(:description, value: protocol.description) %>
   <%= f.hidden_field(:protocol_type, value: protocol.protocol_type) %>
+  <%= f.hidden_field(:visibility) %>
+  <%= f.hidden_field(:default_public_user_role_id) %>
 
 <% end %>
 
diff --git a/app/views/protocol_importers/_preview_modal_footer.html.erb b/app/views/protocol_importers/_preview_modal_footer.html.erb
index e7f5734e4..3c29b8da5 100644
--- a/app/views/protocol_importers/_preview_modal_footer.html.erb
+++ b/app/views/protocol_importers/_preview_modal_footer.html.erb
@@ -1,3 +1,25 @@
-<button type="button" class="btn btn-secondary" data-dismiss="modal"><%=t "general.cancel" %></button>
-<button type="button" class="btn btn-primary" data-action="import_protocol" data-import_type="in_repository_draft"><%=t "protocols.import_export.import_modal.import_to_team_protocols_label" %></button>
-<button type="button" class="btn btn-primary" data-action="import_protocol" data-import_type="in_repository_draft"><%=t "protocols.import_export.import_modal.import_to_private_protocols_label" %></button>
+<div class="footer">
+  <div class="left-section">
+    <div class="default-role-container">
+      <div class="sci-checkbox-container">
+        <%= check_box_tag "visibility", "visible", false, class: "sci-checkbox" %>
+        <span class="sci-checkbox-label"></span>
+      </div>
+      <div class="default-role-description">
+        <%= t("protocols.new_protocol_modal.access_label") %>
+      </div>
+    </div>
+    <div class="hidden" id="roleSelectWrapper">
+      <div class="sci-input-container">
+        <%= label_tag :default_public_user_role_id, t("protocols.new_protocol_modal.role_label") %>
+        <% default_role = UserRole.find_by(name: I18n.t('user_roles.predefined.viewer')).id %>
+        <%= hidden_field_tag :default_public_user_role_id, value: default_role %>
+        <%= select_tag :role_selector, options_for_select(user_roles_collection, default_role) %>
+      </div>
+    </div>
+  </div>
+  <div class="right-section">
+    <button type="button" class="btn btn-secondary" data-dismiss="modal"><%=t "general.cancel" %></button>
+    <button type="button" class="btn btn-primary" data-action="import_protocol" data-import_type="in_repository_draft"><%=t "protocols.import_export.import_modal.import_protocols_label" %></button>
+  </div>
+</div>

From c93c8b4c5b0e4fdcad17cbeee771235835709068 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 09:00:12 +0100
Subject: [PATCH 09/41] Update full-preview-panel data id on protocol-card
 change [SCI-8032]

---
 app/assets/javascripts/protocols/protocolsio.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/assets/javascripts/protocols/protocolsio.js b/app/assets/javascripts/protocols/protocolsio.js
index c03ae7238..69aa6ecc2 100644
--- a/app/assets/javascripts/protocols/protocolsio.js
+++ b/app/assets/javascripts/protocols/protocolsio.js
@@ -34,6 +34,7 @@ function applyClickCallbackOnProtocolCards() {
           $('.full-preview-panel').attr('data-url', currProtocolCard.data('url'));
           $('.full-preview-panel').attr('data-protocol-source', currProtocolCard.data('protocol-source'));
           $('.full-preview-panel').attr('data-id', currProtocolCard.data('id'));
+          $('.full-preview-panel').data('id', currProtocolCard.data('id'));
           $('.convert-protocol').attr('disabled', false);
 
           // Set base tag to account for relative links in the iframe

From 80b3863efa365ecf1e25ac04c541f37841134b0d Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 09:02:17 +0100
Subject: [PATCH 10/41] Render protocol-preview-modal independently on
 protocolio-modal [SCI-8032]

---
 app/views/protocols/index.html.erb                         | 1 +
 app/views/protocols/index/_protocolsio_modal_body.html.erb | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/app/views/protocols/index.html.erb b/app/views/protocols/index.html.erb
index f0443456b..641cdb91f 100644
--- a/app/views/protocols/index.html.erb
+++ b/app/views/protocols/index.html.erb
@@ -43,6 +43,7 @@
 <%= render partial: "protocols/index/linked_children_modal.html.erb" %>
 <%= render partial: "protocols/index/protocolsio_modal.html.erb" %>
 <%= render partial: "protocols/index/new_protocol_modal.html.erb", locals: {type: 'new'} %>
+<%= render partial: "protocols/index/protocol_preview_modal.html.erb" %>
 
 <%= render partial: "protocols/import_export/import_elements.html.erb" %>
 
diff --git a/app/views/protocols/index/_protocolsio_modal_body.html.erb b/app/views/protocols/index/_protocolsio_modal_body.html.erb
index 749d71e25..621d795fd 100644
--- a/app/views/protocols/index/_protocolsio_modal_body.html.erb
+++ b/app/views/protocols/index/_protocolsio_modal_body.html.erb
@@ -98,7 +98,5 @@
   <button type="button" class="btn btn-primary convert-protocol" disabled><%= t('protocols.index.protocolsio.convert') %></button>
 </div>
 
-<%= render partial: "protocols/index/protocol_preview_modal.html.erb" %>
-
 <%= javascript_include_tag "protocols/steps" %>
 <%= javascript_include_tag "protocols/protocolsio.js" %>

From c3066292a0bf58ae33501fbd3e503d0aba9543ec Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 09:17:09 +0100
Subject: [PATCH 11/41] Style the protocol-preview-modal [SCI-8032]

---
 .../stylesheets/protocols/preview_modal.scss  | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/app/assets/stylesheets/protocols/preview_modal.scss b/app/assets/stylesheets/protocols/preview_modal.scss
index 2613d169d..1c4dade34 100644
--- a/app/assets/stylesheets/protocols/preview_modal.scss
+++ b/app/assets/stylesheets/protocols/preview_modal.scss
@@ -26,4 +26,43 @@
   .general-error {
     text-align: center;
   }
+
+  .modal-footer {
+    .footer {
+      display: flex;
+      justify-content: space-between;
+      align-items: center;
+
+      .left-section {
+        display: flex;
+        justify-content: space-between;
+        column-gap: 32px;
+
+        .default-role-container {
+          display: flex;
+          align-items: center;
+          column-gap: 8px;
+        }
+
+        .sci-input-container {
+          display: flex;
+          align-items: center;
+          flex-grow: 1;
+          column-gap: 12px;
+
+          label {
+            white-space: nowrap;
+            margin-bottom: 0;
+          }
+        }
+      }
+
+      .right-section {
+        display: flex;
+        justify-content: flex-end;
+        flex-basis: 0;
+        column-gap: 8px;
+      }
+    }
+  }
 }

From 515baa8de70b38ac6a9faff9fb65657c578750b7 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 11:03:04 +0100
Subject: [PATCH 12/41] Update translations [SCI-8032]

---
 config/locales/en.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index b51ae89b7..b1ecac58d 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -2641,6 +2641,7 @@ en:
         import: "Load"
         import_to_team_protocols_label: "Import to Team Protocols"
         import_to_private_protocols_label: "Import to My Protocols"
+        import_protocols_label: "Import"
     export:
       export_results:
         title: "Export results"
@@ -2848,7 +2849,7 @@ en:
         import:
           public: "Team protocols"
           private: "My protocols"
-          success_flash: 'Protocol <strong>%{name}</strong> successfully imported to %{type}.'
+          success_flash: 'Protocol <strong>%{name}</strong> successfully imported.'
 
     steps:
       placeholder: 'Enter step name'

From 0cd31d451d9eb1915e59b6b339088853db500805 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 11:06:12 +0100
Subject: [PATCH 13/41] Fix hound [SCI-8032]

---
 .../stylesheets/protocols/preview_modal.scss     | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/app/assets/stylesheets/protocols/preview_modal.scss b/app/assets/stylesheets/protocols/preview_modal.scss
index 1c4dade34..424cebbf2 100644
--- a/app/assets/stylesheets/protocols/preview_modal.scss
+++ b/app/assets/stylesheets/protocols/preview_modal.scss
@@ -29,39 +29,39 @@
 
   .modal-footer {
     .footer {
+      align-items: center;
       display: flex;
       justify-content: space-between;
-      align-items: center;
 
       .left-section {
+        column-gap: 32px;
         display: flex;
         justify-content: space-between;
-        column-gap: 32px;
 
         .default-role-container {
-          display: flex;
           align-items: center;
           column-gap: 8px;
+          display: flex;
         }
 
         .sci-input-container {
           display: flex;
           align-items: center;
-          flex-grow: 1;
           column-gap: 12px;
+          flex-grow: 1;
 
           label {
-            white-space: nowrap;
             margin-bottom: 0;
+            white-space: nowrap;
           }
         }
       }
 
       .right-section {
-        display: flex;
-        justify-content: flex-end;
-        flex-basis: 0;
         column-gap: 8px;
+        display: flex;
+        flex-basis: 0;
+        justify-content: flex-end;
       }
     }
   }

From 73ed75a73acdc6eba4b09396d87cff691bbd0b1d Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Fri, 3 Mar 2023 13:20:15 +0100
Subject: [PATCH 14/41] Ensure user assignments stay in sync with protocol
 versions [SCI-8060]

---
 app/models/concerns/assignable.rb |  5 +++++
 app/models/protocol.rb            | 28 ++++++++++++++++++++++++++++
 app/models/user_assignment.rb     |  5 +++++
 3 files changed, 38 insertions(+)

diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index 54fc2c390..d091c5a43 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -58,6 +58,11 @@ module Assignable
       self.class.name.in?(Extends::TOP_LEVEL_ASSIGNABLES)
     end
 
+    def after_user_assignment_save
+      # Optional, redefine in the assignable model.
+      # Will be called when an assignment is saved for the assignable model.
+    end
+
     private
 
     def create_users_assignments
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 984abd404..e269bd525 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -17,6 +17,7 @@ class Protocol < ApplicationRecord
   include TinyMceImages
 
   after_create :auto_assign_protocol_members, if: :visible?
+  after_create :sync_child_protocol_user_assignments, unless: -> { parent_id }
   after_destroy :decrement_linked_children
   after_save :update_user_assignments, if: -> { saved_change_to_visibility? && in_repository? }
   after_save :update_linked_children
@@ -684,8 +685,35 @@ class Protocol < ApplicationRecord
     end
   end
 
+  def after_user_assignment_save
+    sync_child_protocol_user_assignments
+  end
+
   private
 
+  def sync_child_protocol_user_assignments
+    # Copy user assignments to child protocols
+
+    return if parent_id
+
+    Protocol.transaction do
+      user_assignments.find_each do |user_assignment|
+        linked_children.find_each do |child_protocol|
+          child_protocol.user_assignments.find_or_initialize_by(
+            user: user_assignment.user
+          ).update!(
+            user_assignment.attributes.slice(
+              'user_role_id',
+              'assigned',
+              'assigned_by_id',
+              'team_id'
+            )
+          )
+        end
+      end
+    end
+  end
+
   def auto_assign_protocol_members
     UserAssignments::ProtocolGroupAssignmentJob.perform_now(
       team,
diff --git a/app/models/user_assignment.rb b/app/models/user_assignment.rb
index fa09bd1a7..921669ba5 100644
--- a/app/models/user_assignment.rb
+++ b/app/models/user_assignment.rb
@@ -7,6 +7,7 @@ class UserAssignment < ApplicationRecord
   after_create :assign_team_child_objects, if: -> { assignable.is_a?(Team) }
   after_update :update_team_children_assignments, if: -> { assignable.is_a?(Team) && saved_change_to_user_role_id? }
   before_destroy :unassign_team_child_objects, if: -> { assignable.is_a?(Team) }
+  after_save :call_user_assignment_save_hook
 
   belongs_to :assignable, polymorphic: true, touch: true
   belongs_to :user_role
@@ -24,6 +25,10 @@ class UserAssignment < ApplicationRecord
 
   private
 
+  def call_user_assignment_save_hook
+    assignable.after_user_assignment_save
+  end
+
   def assign_team_child_objects
     UserAssignments::CreateTeamUserAssignmentsService.new(self).call
   end

From 9e33fae006c0fb4771cc3a4af8782f6a61e5b195 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 15:59:29 +0100
Subject: [PATCH 15/41] Make table cell single lined and limit the max width
 [SCI-7996]

---
 app/assets/stylesheets/protocols/index.scss | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/app/assets/stylesheets/protocols/index.scss b/app/assets/stylesheets/protocols/index.scss
index 893ff3eeb..146297bc0 100644
--- a/app/assets/stylesheets/protocols/index.scss
+++ b/app/assets/stylesheets/protocols/index.scss
@@ -18,6 +18,15 @@
       flex-direction: column;
       height: 100%;
       width: 100%;
+
+      tbody {
+        td:not(:first-child) {
+          white-space: nowrap;
+          overflow: hidden;
+          text-overflow: ellipsis;
+          max-width: 30rem;
+        }
+      }
     }
 
     .toolbar {

From c036c722437be8df21e7d2707fdda1e5237413b9 Mon Sep 17 00:00:00 2001
From: sboursen-scinote <soufiane@scinote.net>
Date: Fri, 3 Mar 2023 16:00:50 +0100
Subject: [PATCH 16/41] Fix hound [SCI-7996]

---
 app/assets/stylesheets/protocols/index.scss | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/assets/stylesheets/protocols/index.scss b/app/assets/stylesheets/protocols/index.scss
index 146297bc0..157c68fa2 100644
--- a/app/assets/stylesheets/protocols/index.scss
+++ b/app/assets/stylesheets/protocols/index.scss
@@ -21,10 +21,10 @@
 
       tbody {
         td:not(:first-child) {
-          white-space: nowrap;
+          max-width: 30rem;
           overflow: hidden;
           text-overflow: ellipsis;
-          max-width: 30rem;
+          white-space: nowrap;
         }
       }
     }

From 3fd793715487f98092d369d8a44d35a4ba50f7a1 Mon Sep 17 00:00:00 2001
From: Giga Chubinidze <gchubinidze@unisens.ge>
Date: Sun, 5 Mar 2023 02:25:25 +0400
Subject: [PATCH 17/41] CSS: Incorrect paddings in the "Protocol info" modal
 [SCI-8054]

---
 app/assets/stylesheets/my_modules/protocols/index.scss | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/assets/stylesheets/my_modules/protocols/index.scss b/app/assets/stylesheets/my_modules/protocols/index.scss
index 6fe56daac..9f03457f0 100644
--- a/app/assets/stylesheets/my_modules/protocols/index.scss
+++ b/app/assets/stylesheets/my_modules/protocols/index.scss
@@ -426,6 +426,7 @@
     left: -125px;
     max-width: 100vw;
     width: 506px;
+    padding: 15px 0;
 
     .dropdown-header,
     .dropdown-body {

From 9379d9a175134ab1fc99629dc9b26d2a20d00ae8 Mon Sep 17 00:00:00 2001
From: ajugo <andrej.jugovic7@gmail.com>
Date: Mon, 6 Mar 2023 10:53:01 +0100
Subject: [PATCH 18/41] Fix load protocol to task [SCI-8072] (#5070)

---
 app/controllers/protocols_controller.rb | 8 ++++----
 app/datatables/protocols_datatable.rb   | 1 +
 app/models/protocol.rb                  | 4 ++++
 app/utilities/protocols_exporter.rb     | 2 +-
 app/utilities/protocols_exporter_v2.rb  | 2 +-
 5 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index fc23f84f5..bd5be2e73 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -530,7 +530,7 @@ class ProtocolsController < ApplicationController
                           else
                             @protocol.parent.parent
                           end
-          @protocol.update_from_parent(current_user, source_parent.latest_published_version)
+          @protocol.update_from_parent(current_user, source_parent.latest_published_version_or_self)
         rescue StandardError
           transaction_error = true
           raise ActiveRecord::Rollback
@@ -813,7 +813,7 @@ class ProtocolsController < ApplicationController
 
           # Create folder and xml file for each protocol and populate it
           @protocols.each do |protocol|
-            protocol = protocol.latest_published_version || protocol
+            protocol = protocol.latest_published_version_or_self
             protocol_dir = get_guid(protocol.id).to_s
             ostream.put_next_entry("#{protocol_dir}/eln.xml")
             ostream.print(generate_protocol_xml(protocol))
@@ -1173,7 +1173,7 @@ class ProtocolsController < ApplicationController
   def check_clone_permissions
     load_team_and_type
     protocol = Protocol.find_by(id: params[:ids][0])
-    @original = protocol.latest_published_version || protocol
+    @original = protocol.latest_published_version_or_self
 
     if @original.blank? ||
        !can_clone_protocol_in_repository?(@original) || @type == :archive
@@ -1251,7 +1251,7 @@ class ProtocolsController < ApplicationController
 
   def check_load_from_repository_permissions
     @protocol = Protocol.find_by(id: params[:id])
-    @source = Protocol.find_by(id: params[:source_id])&.latest_published_version
+    @source = Protocol.find_by(id: params[:source_id])&.latest_published_version_or_self
 
     render_403 unless @protocol.present? && @source.present? &&
                       (can_manage_protocol_in_module?(@protocol) &&
diff --git a/app/datatables/protocols_datatable.rb b/app/datatables/protocols_datatable.rb
index 8cfb621a0..e6b7dcc5e 100644
--- a/app/datatables/protocols_datatable.rb
+++ b/app/datatables/protocols_datatable.rb
@@ -144,6 +144,7 @@ class ProtocolsDatatable < CustomDatatable
                                      .select(:id)
     published_versions = @team.protocols
                               .where(protocol_type: Protocol.protocol_types[:in_repository_published_version])
+                              .order(:parent_id, version_number: :desc)
                               .select('DISTINCT ON (parent_id) id')
     new_drafts = @team.protocols
                       .where(protocol_type: Protocol.protocol_types[:in_repository_draft], parent_id: nil)
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 7852851e1..221c6752d 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -260,6 +260,10 @@ class Protocol < ApplicationRecord
     in_repository_draft? && parent.blank?
   end
 
+  def latest_published_version_or_self
+    latest_published_version || self
+  end
+
   def permission_parent
     in_module? ? my_module : team
   end
diff --git a/app/utilities/protocols_exporter.rb b/app/utilities/protocols_exporter.rb
index 384606514..83e785338 100644
--- a/app/utilities/protocols_exporter.rb
+++ b/app/utilities/protocols_exporter.rb
@@ -27,7 +27,7 @@ module ProtocolsExporter
     envelope_xml = "<envelope xmlns=\"http://www.scinote.net\" " \
                    "version=\"1.0\">\n"
     protocols.each do |protocol|
-      protocol = protocol.latest_published_version || protocol
+      protocol = protocol.latest_published_version_or_self
       protocol_name = get_protocol_name(protocol)
       envelope_xml << "<protocol id=\"#{protocol.id}\" " \
                       "guid=\"#{get_guid(protocol.id)}\">#{protocol_name}" \
diff --git a/app/utilities/protocols_exporter_v2.rb b/app/utilities/protocols_exporter_v2.rb
index dd8b6f165..537e22cda 100644
--- a/app/utilities/protocols_exporter_v2.rb
+++ b/app/utilities/protocols_exporter_v2.rb
@@ -9,7 +9,7 @@ module ProtocolsExporterV2
     envelope_xml = "<envelope xmlns=\"http://www.scinote.net\" " \
                    "version=\"1.1\">\n"
     protocols.each do |protocol|
-      protocol = protocol.latest_published_version || protocol
+      protocol = protocol.latest_published_version_or_self
       protocol_name = get_protocol_name(protocol)
       envelope_xml << "<protocol id=\"#{protocol.id}\" " \
                       "guid=\"#{get_guid(protocol.id)}\">#{protocol_name}" \

From 9d4e212c7dad1ec0093770330613d6cd8b940372 Mon Sep 17 00:00:00 2001
From: ajugo <andrej.jugovic7@gmail.com>
Date: Mon, 6 Mar 2023 11:50:37 +0100
Subject: [PATCH 19/41] Fix protocol template access filter [SCI-7988] (#5073)

---
 app/datatables/protocols_datatable.rb | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/app/datatables/protocols_datatable.rb b/app/datatables/protocols_datatable.rb
index e6b7dcc5e..234bcdaa4 100644
--- a/app/datatables/protocols_datatable.rb
+++ b/app/datatables/protocols_datatable.rb
@@ -120,7 +120,13 @@ class ProtocolsDatatable < CustomDatatable
     records = records.where('protocols.updated_at > ?', params[:modified_on_from]) if params[:modified_on_from].present?
     records = records.where('protocols.updated_at < ?', params[:modified_on_to]) if params[:modified_on_to].present?
     records = records.where(protocols: { published_by_id: params[:published_by] }) if params[:published_by].present?
-    records = records.where(all_user_assignments: { user_id: params[:members] }) if params[:members].present?
+
+    if params[:members].present?
+      records = records.joins('LEFT OUTER JOIN "user_assignments" "all_user_assignments" '\
+                              'ON "all_user_assignments"."assignable_type" = \'Protocol\' '\
+                              'AND "all_user_assignments"."assignable_id" = "protocols"."id"')
+                       .where(all_user_assignments: { user_id: params[:members] })
+    end
 
     if params[:archived_on_from].present?
       records = records.where('protocols.archived_on > ?', params[:archived_on_from])

From 47c59ecc6c89c345ec8ec84a1b40aec702a42237 Mon Sep 17 00:00:00 2001
From: aignatov-bio <47317017+aignatov-bio@users.noreply.github.com>
Date: Mon, 6 Mar 2023 11:51:40 +0100
Subject: [PATCH 20/41] Fix protocol copy/save message [SCI-8064] (#5079)

---
 config/locales/en.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index c7962aba8..d1e67e82a 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1099,7 +1099,7 @@ en:
       update_parent_flash: "Protocol in templates was successfully updated with the version from the task."
       update_parent_error: "Failed to update templates version of the protocol."
       update_parent_error_locked: "Failed to update templates version of the protocol. One or more files in the protocol are currently being edited."
-      update_from_parent_flash: "Version in the templates was successfully updated."
+      update_from_parent_flash: "Protocol was successfully updated."
       update_from_parent_error: "Failed to update the protocol with the version in the templates."
       update_from_parent_error_locked: "Failed to update the protocol with the version in the templates. One or more files in the protocol are currently being edited."
       load_from_repository_flash: "Successfully loaded the protocol from the templates."
@@ -1130,7 +1130,7 @@ en:
         link_label: "Link task to this protocol in templates"
         link_text: "<strong>Warning!</strong>&nbsp;This will unlink the currently linked protocol."
         error_400: "Due to unknown error, protocol could not be copied to templates."
-        success_message: "New protocol template was successfully saved. You can see it in protocol templates."
+        success_message: "Protocol was successfully saved as a new protocol template."
         confirm: "Save"
       load_from_file_flash: "Successfully loaded the protocol from the file."
       load_from_file_error: "Failed to load the protocol from file."

From cfcb80f64235e665fd82b66847e63caa1d0d496b Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 6 Mar 2023 16:06:38 +0100
Subject: [PATCH 21/41] Fix assignment sync to new protocol drafts and deletion
 [SCI-8060]

---
 .../generate_user_assignments_job.rb          | 10 ++++
 app/models/concerns/assignable.rb             | 10 ++--
 app/models/protocol.rb                        | 60 ++++++++++++-------
 app/models/user_assignment.rb                 |  7 ++-
 4 files changed, 56 insertions(+), 31 deletions(-)

diff --git a/app/jobs/user_assignments/generate_user_assignments_job.rb b/app/jobs/user_assignments/generate_user_assignments_job.rb
index 884a940c2..dd49489e2 100644
--- a/app/jobs/user_assignments/generate_user_assignments_job.rb
+++ b/app/jobs/user_assignments/generate_user_assignments_job.rb
@@ -46,6 +46,16 @@ module UserAssignments
     end
 
     def assign_users_to_protocol(protocol)
+      if protocol.parent_id && protocol.in_repository_draft?
+        Protocol.transaction(requires_new: true) do
+          protocol.parent.user_assignments.find_each do |user_assignment|
+            protocol.parent.sync_child_protocol_user_assignment(user_assignment, protocol.id)
+          end
+        end
+
+        return
+      end
+
       return unless protocol.visible?
 
       protocol.create_public_user_assignments!(@assigned_by)
diff --git a/app/models/concerns/assignable.rb b/app/models/concerns/assignable.rb
index d091c5a43..7f70e4020 100644
--- a/app/models/concerns/assignable.rb
+++ b/app/models/concerns/assignable.rb
@@ -58,13 +58,13 @@ module Assignable
       self.class.name.in?(Extends::TOP_LEVEL_ASSIGNABLES)
     end
 
-    def after_user_assignment_save
-      # Optional, redefine in the assignable model.
-      # Will be called when an assignment is saved for the assignable model.
-    end
-
     private
 
+    def after_user_assignment_changed(user_assignment = nil)
+      # Optional, redefine in the assignable model.
+      # Will be called when an assignment is changed (save/destroy) for the assignable model.
+    end
+
     def create_users_assignments
       return if skip_user_assignments
 
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index e269bd525..4dbbb9c56 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -17,7 +17,6 @@ class Protocol < ApplicationRecord
   include TinyMceImages
 
   after_create :auto_assign_protocol_members, if: :visible?
-  after_create :sync_child_protocol_user_assignments, unless: -> { parent_id }
   after_destroy :decrement_linked_children
   after_save :update_user_assignments, if: -> { saved_change_to_visibility? && in_repository? }
   after_save :update_linked_children
@@ -685,33 +684,48 @@ class Protocol < ApplicationRecord
     end
   end
 
-  def after_user_assignment_save
-    sync_child_protocol_user_assignments
+  def child_version_protocols
+    published_versions.or(Protocol.where(id: draft&.id))
+  end
+
+  def sync_child_protocol_user_assignment(user_assignment, child_protocol_id = nil)
+    # Copy user assignments to child protocol(s)
+
+    Protocol.transaction(requires_new: true) do
+      # Reload to ensure a potential new draft is also included in child versions
+      reload
+
+      (
+        # all or single child version protocol
+        child_protocol_id ? child_version_protocols.where(id: child_protocol_id) : child_version_protocols
+      ).find_each do |child_protocol|
+        child_assignment = child_protocol.user_assignments.find_or_initialize_by(
+          user: user_assignment.user
+        )
+
+        if user_assignment.destroyed?
+          child_assignment.destroy! if child_assignment.persisted?
+          next
+        end
+
+        child_assignment.update!(
+          user_assignment.attributes.slice(
+            'user_role_id',
+            'assigned',
+            'assigned_by_id',
+            'team_id'
+          )
+        )
+      end
+    end
   end
 
   private
 
-  def sync_child_protocol_user_assignments
-    # Copy user assignments to child protocols
+  def after_user_assignment_changed(user_assignment)
+    return unless in_repository_published_original?
 
-    return if parent_id
-
-    Protocol.transaction do
-      user_assignments.find_each do |user_assignment|
-        linked_children.find_each do |child_protocol|
-          child_protocol.user_assignments.find_or_initialize_by(
-            user: user_assignment.user
-          ).update!(
-            user_assignment.attributes.slice(
-              'user_role_id',
-              'assigned',
-              'assigned_by_id',
-              'team_id'
-            )
-          )
-        end
-      end
-    end
+    sync_child_protocol_user_assignment(user_assignment)
   end
 
   def auto_assign_protocol_members
diff --git a/app/models/user_assignment.rb b/app/models/user_assignment.rb
index 921669ba5..9b54a5479 100644
--- a/app/models/user_assignment.rb
+++ b/app/models/user_assignment.rb
@@ -7,7 +7,8 @@ class UserAssignment < ApplicationRecord
   after_create :assign_team_child_objects, if: -> { assignable.is_a?(Team) }
   after_update :update_team_children_assignments, if: -> { assignable.is_a?(Team) && saved_change_to_user_role_id? }
   before_destroy :unassign_team_child_objects, if: -> { assignable.is_a?(Team) }
-  after_save :call_user_assignment_save_hook
+  after_destroy :call_user_assignment_changed_hook
+  after_save :call_user_assignment_changed_hook
 
   belongs_to :assignable, polymorphic: true, touch: true
   belongs_to :user_role
@@ -25,8 +26,8 @@ class UserAssignment < ApplicationRecord
 
   private
 
-  def call_user_assignment_save_hook
-    assignable.after_user_assignment_save
+  def call_user_assignment_changed_hook
+    assignable.__send__(:after_user_assignment_changed, self)
   end
 
   def assign_team_child_objects

From 2f29477e02db05ae057c4fe51594fea8899ab25c Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Mon, 6 Mar 2023 16:43:46 +0100
Subject: [PATCH 22/41] Protocol/general user assignment changes and fixes
 [SCI-8039]

---
 .../access_permissions/user_assignments.js    |  4 +-
 .../access_permissions/access_modal.scss      | 17 +++++++--
 .../shared_styles/elements/dropdown.scss      |  4 ++
 .../shared_styles/elements/modal.scss         | 18 +++++++++
 .../protocols_controller.rb                   | 17 ++++++---
 .../modals/_edit_modal.html.erb               | 16 ++++----
 .../modals/_show_modal.html.erb               |  4 +-
 .../_default_public_user_role_form.html.erb   | 38 +++++++++++++------
 .../partials/_member_field.html.erb           |  7 ++--
 .../partials/_new_assignments_form.html.erb   |  2 +-
 .../partials/_user_assignment_field.html.erb  |  2 +-
 .../protocols/new.json.jbuilder               |  2 +-
 .../protocols/show.json.jbuilder              |  7 ++--
 13 files changed, 96 insertions(+), 42 deletions(-)

diff --git a/app/assets/javascripts/access_permissions/user_assignments.js b/app/assets/javascripts/access_permissions/user_assignments.js
index c636345d9..d9d796ad0 100644
--- a/app/assets/javascripts/access_permissions/user_assignments.js
+++ b/app/assets/javascripts/access_permissions/user_assignments.js
@@ -8,7 +8,7 @@
       let submitBtn = $(this).find('input[type="submit"]');
 
       $(this).find('input:checked').each((_, el) => {
-        let select = $(el).closest('.row').find('select');
+        let select = $(el).closest('.new-member-item').find('select');
         let selectValue = parseInt(select.val(), 10);
         values.push(selectValue);
         count += 1;
@@ -48,7 +48,7 @@
 
     $(document).on('click', '.user-assignment-dropdown .user-role-selector', function() {
       let roleId = $(this).data('role-id');
-      $(this).closest('.dropdown').find('#user_assignment_user_role_id').val(roleId);
+      $(this).closest('.dropdown').find('#user_assignment_user_role_id, .default-public-user-role-id').val(roleId);
       $(this).closest('form').trigger('submit');
     });
   }
diff --git a/app/assets/stylesheets/access_permissions/access_modal.scss b/app/assets/stylesheets/access_permissions/access_modal.scss
index fb30a0052..d83980af2 100644
--- a/app/assets/stylesheets/access_permissions/access_modal.scss
+++ b/app/assets/stylesheets/access_permissions/access_modal.scss
@@ -1,4 +1,17 @@
 #user_assignments_modal {
+
+  .btn-role-select {
+    padding: 0;
+
+    &:hover {
+      background-color: $color-white;
+    }
+
+    &:focus {
+      box-shadow: none;
+    }
+  }
+
   .modal-body {
     min-height: calc(100vh - 200px);
     overflow: auto;
@@ -7,9 +20,7 @@
 
   .member-item {
     border-bottom: 1px solid $modal-header-border-color;
-
-    margin: 0 .5em;
-    padding: .5em;
+    padding: .5em 0;
   }
 
   .user-assignment-role .dropdown-toggle,
diff --git a/app/assets/stylesheets/shared_styles/elements/dropdown.scss b/app/assets/stylesheets/shared_styles/elements/dropdown.scss
index 6b57e2b5f..a1f8bf9b5 100644
--- a/app/assets/stylesheets/shared_styles/elements/dropdown.scss
+++ b/app/assets/stylesheets/shared_styles/elements/dropdown.scss
@@ -2,6 +2,10 @@
 
 @import "constants";
 
+.dropdown-menu .divider {
+  margin: 5px 0;
+}
+
 .sci-dropdown {
   [data-toggle="dropdown"] {
     .caret {
diff --git a/app/assets/stylesheets/shared_styles/elements/modal.scss b/app/assets/stylesheets/shared_styles/elements/modal.scss
index 61fc5369f..b843df47d 100644
--- a/app/assets/stylesheets/shared_styles/elements/modal.scss
+++ b/app/assets/stylesheets/shared_styles/elements/modal.scss
@@ -7,6 +7,24 @@
 }
 
 .modal {
+  .modal-dialog {
+    .modal-body {
+      padding: 0;
+    }
+
+    .modal-content {
+      padding: 1.15em;
+    }
+
+    .modal-header {
+      padding: 0 0 1.15em 0;
+    }
+
+    .modal-footer {
+      padding: 1.15em 0 0 0;
+    }
+  }
+
   .modal-absolute-close-button {
     position: absolute;
     right: 1em;
diff --git a/app/controllers/access_permissions/protocols_controller.rb b/app/controllers/access_permissions/protocols_controller.rb
index 88885fe27..77a84113f 100644
--- a/app/controllers/access_permissions/protocols_controller.rb
+++ b/app/controllers/access_permissions/protocols_controller.rb
@@ -51,12 +51,17 @@ module AccessPermissions
         permitted_create_params[:resource_members].each do |_k, user_assignment_params|
           next unless user_assignment_params[:assign] == '1'
 
-          user_assignment = UserAssignment.new(user_assignment_params)
-          user_assignment.assignable = @protocol
-          user_assignment.assigned = :manually
-          user_assignment.team = current_team
-          user_assignment.assigned_by = current_user
-          user_assignment.save!
+          user_assignment = UserAssignment.find_or_initialize_by(
+            assignable: @protocol,
+            user_id: user_assignment_params[:user_id],
+            team: current_team
+          )
+
+          user_assignment.update!(
+            user_role_id: user_assignment_params[:user_role_id],
+            assigned_by: current_user,
+            assigned: :manually
+          )
 
           created_count += 1
           log_activity(:protocol_template_access_granted, user_assignment)
diff --git a/app/views/access_permissions/modals/_edit_modal.html.erb b/app/views/access_permissions/modals/_edit_modal.html.erb
index 242759a82..b7b9ff22c 100644
--- a/app/views/access_permissions/modals/_edit_modal.html.erb
+++ b/app/views/access_permissions/modals/_edit_modal.html.erb
@@ -1,7 +1,7 @@
 <% # frozen_string_literal: true %>
 
 <div class="modal fade user-assignments-modal <%= assignable.class.name.parameterize(separator: '-') %>-assignments-modal" tabindex="-1" role="dialog" data-action="modal-close">
-  <div class="modal-dialog modal-lg" role="document">
+  <div class="modal-dialog" role="document">
     <div class="modal-content" id="user_assignments_modal">
       <div class="modal-header">
         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
@@ -9,19 +9,19 @@
       </div>
       <div class="modal-body">
         <% manually_assigned_users.order(full_name: :asc).each do |user| %>
-          <%= render('access_permissions/partials/member_field',
-                    user: user,
-                    assignable: assignable,
-                    update_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable),
-                    delete_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable, user_id: user.id)
-          ) %>
+          <%
+            options = { user: user, with_inherit: !assignable.top_level_assignable?, assignable: assignable, update_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable) }
+            options.merge!(delete_path: public_send("access_permissions_#{assignable.class.name.underscore}_path", assignable, user_id: user.id)) if assignable == top_level_assignable
+          %>
+
+          <%= render('access_permissions/partials/member_field', options) %>
         <% end %>
         <%= render('access_permissions/partials/default_public_user_role_form', assignable: top_level_assignable, editable: assignable == top_level_assignable) if top_level_assignable.respond_to?(:visible?) && top_level_assignable.visible? %>
       </div>
 
       <% if assignable.top_level_assignable? %>
         <div class="modal-footer">
-          <%= link_to new_assignment_path, class: 'btn btn-default pull-left', data: { action: 'swap-remote-container', target: '#user_assignments_modal' } do %>
+          <%= link_to new_assignment_path, class: 'btn btn-default pull-right', data: { action: 'swap-remote-container', target: '#user_assignments_modal' } do %>
             <i class="fas fa-plus"></i>
             <%= t('access_permissions.grant_access') %>
           <% end %>
diff --git a/app/views/access_permissions/modals/_show_modal.html.erb b/app/views/access_permissions/modals/_show_modal.html.erb
index 648e0cee9..5ca328499 100644
--- a/app/views/access_permissions/modals/_show_modal.html.erb
+++ b/app/views/access_permissions/modals/_show_modal.html.erb
@@ -1,11 +1,11 @@
 <% # frozen_string_literal: true %>
 
 <div class="modal fade <%= assignable.class.name.parameterize(separator: '-') %>-assignments-modal" tabindex="-1" role="dialog" data-action="modal-close">
-  <div class="modal-dialog modal-lg" role="document">
+  <div class="modal-dialog" role="document">
     <div class="modal-content" id="user_assignments_modal">
       <div class="modal-header">
         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-        <h4 class="modal-title"><%= t "access_permissions.#{assignable.class.name.pluralize.underscore}.modals.show_modal.title", assignable_name: assignable.name %></h4>
+        <h4 class="modal-title"><%= t "access_permissions.#{assignable.class.name.pluralize.underscore}.modals.show_modal.title", resource_name: assignable.name %></h4>
       </div>
       <div class="modal-body">
         <% manually_assigned_users.order(full_name: :asc).each do |user| %>
diff --git a/app/views/access_permissions/partials/_default_public_user_role_form.html.erb b/app/views/access_permissions/partials/_default_public_user_role_form.html.erb
index 8f65da4d4..2fa1254ec 100644
--- a/app/views/access_permissions/partials/_default_public_user_role_form.html.erb
+++ b/app/views/access_permissions/partials/_default_public_user_role_form.html.erb
@@ -1,5 +1,5 @@
 <% if assignable.visible? %>
-  <%= form_with(model: assignable, url: [:update_default_public_user_role, :access_permissions, assignable], method: :put, remote: true, html: { class: 'row member-item', id: 'public_assignments', data: { action: 'replace-form autosave-form', object_type: assignable.class.name.underscore.to_sym } }) do |f| %>
+  <%= form_with(model: assignable, url: [:update_default_public_user_role, :access_permissions, assignable], method: :put, remote: true, html: { class: 'member-item', id: 'public_assignments', data: { action: 'replace-form autosave-form', object_type: assignable.class.name.underscore.to_sym } }) do |f| %>
     <div class="user-assignment-info">
       <div class="global-avatar-container">
         <%= image_tag "icon/team.png", class: 'img-circle pull-left' %>
@@ -7,20 +7,36 @@
       <div>
         <%= t('access_permissions.everyone_else', team_name: assignable.team.name) %>
         <%= render 'access_permissions/partials/public_members_dropdown', team: assignable.team, assignable: assignable %>
-        <br>
-        <small class="text-muted">
-          <%= assignable.default_public_user_role.name %>
-          <span class="permission-object-tag" title="<%= t("access_permissions.partials.#{assignable.class.name.underscore}_tooltip") %>"">
-            <%= t("access_permissions.partials.#{assignable.class.name.underscore}") %>
-          </span>
-        </small>
       </div>
     </div>
     <div class="user-assignment-controls">
       <div class="user-assignment-role">
-        <% if editable %>
-          <%= f.select :default_public_user_role_id, options_for_select(user_roles_collection + [[t('access_permissions.remove_access'), nil]], selected: assignable.default_public_user_role_id), {}, class: 'form-control selectpicker', title: t("user_assignment.change_#{assignable.class.name.underscore}_role"), data: { 'selected-text-format' => 'static' } %>
-        <% end %>
+        <div class="user-assignment-controls">
+          <div class="dropdown pull-right">
+            <button class="btn btn-light btn-role-select" type="button" id="defaultPublicUserRole" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
+              <%= f.object.default_public_user_role.name %>
+              <span class="caret"></span>
+            </button>
+            <%= f.hidden_field :default_public_user_role_id, value: f.object.default_public_user_role.id, class: "default-public-user-role-id" %>
+            <ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="defaultPublicUserRole">
+              <% user_roles_collection.each do |role| %>
+                <li>
+                  <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
+                    <%= role[0] %>
+                  </a>
+                </li>
+              <% end %>
+              <% if assignable.top_level_assignable?  %>
+                <li role="separator" class="divider" data-hook="support-dropdown-separator"></li>
+                <li>
+                  <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="">
+                    <%= t('access_permissions.remove_access') %>
+                  </a>
+                </li>
+              <% end %>
+            </ul>
+          </div>
+        </div>
       </div>
     </div>
   <% end %>
diff --git a/app/views/access_permissions/partials/_member_field.html.erb b/app/views/access_permissions/partials/_member_field.html.erb
index bc1cee7a8..62e18081e 100644
--- a/app/views/access_permissions/partials/_member_field.html.erb
+++ b/app/views/access_permissions/partials/_member_field.html.erb
@@ -1,6 +1,7 @@
 <% # frozen_string_literal: true %>
 
 <%
+  with_inherit ||= false
   assignment = assignable.user_assignments.find_by(user_id: user.id, team: current_team)
   item_id = dom_id(user, :assignment_member)
 %>
@@ -18,15 +19,15 @@
       </div>
     </div>
     <div class="user-assignment-controls">
-      <% unless defined?(with_inherit) && current_user == user %>
+      <% unless with_inherit && current_user == user %>
         <div class="dropdown pull-right">
-          <button class="btn btn-light" type="button" id="userAccess_<%= user.id %>" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
+          <button class="btn btn-light btn-role-select" type="button" id="userAccess_<%= user.id %>" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
             <%= f.object.user_role.name %>
             <span class="caret"></span>
           </button>
           <%= f.hidden_field :user_role_id, value: f.object.user_role.id %>
           <ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="userAccess_<%= user.id %>">
-            <% user_roles_collection(with_inherit: defined? with_inherit).each do |role| %>
+            <% user_roles_collection(with_inherit: with_inherit).each do |role| %>
               <li>
                 <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
                   <%= role[0] %>
diff --git a/app/views/access_permissions/partials/_new_assignments_form.html.erb b/app/views/access_permissions/partials/_new_assignments_form.html.erb
index fc2bf4c56..31c181740 100644
--- a/app/views/access_permissions/partials/_new_assignments_form.html.erb
+++ b/app/views/access_permissions/partials/_new_assignments_form.html.erb
@@ -1,6 +1,6 @@
 <% # frozen_string_literal: true %>
 
-<div class="modal-content" id="user_assignments_modal" data-action="modal-close" data-target="<%= projects_path %>">
+<div class="modal-content" id="user_assignments_modal" data-action="modal-close" data-target="<%= public_send("#{assignable.class.name.pluralize.underscore}_path") %>">
   <div class="modal-header">
     <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
     <h4 class="modal-title">
diff --git a/app/views/access_permissions/partials/_user_assignment_field.html.erb b/app/views/access_permissions/partials/_user_assignment_field.html.erb
index 700034dde..4d7607482 100644
--- a/app/views/access_permissions/partials/_user_assignment_field.html.erb
+++ b/app/views/access_permissions/partials/_user_assignment_field.html.erb
@@ -5,7 +5,7 @@
   id = dom_id(user, :new_protocol_member)
 %>
 
-<div class="row member-item new-member-item" data-filter-item="<%= user.full_name %>">
+<div class="member-item new-member-item" data-filter-item="<%= user.full_name %>">
   <%= user_form.hidden_field :user_id, value: user.id, name:"access_permissions_new_user_form[resource_members][#{user.id}][user_id]"  %>
   <div class="user-assignment-info">
     <div class="sci-checkbox-container">
diff --git a/app/views/access_permissions/protocols/new.json.jbuilder b/app/views/access_permissions/protocols/new.json.jbuilder
index e105a5971..c626e01fe 100644
--- a/app/views/access_permissions/protocols/new.json.jbuilder
+++ b/app/views/access_permissions/protocols/new.json.jbuilder
@@ -6,7 +6,7 @@ json.html controller.render_to_string(
   locals: {
     assignable: @protocol,
     form_object: @user_assignment,
-    users: current_team.users.where.not(id: @protocol.assigned_users.select(:id)),
+    users: current_team.users.where.not(id: @protocol.manually_assigned_users.select(:id)),
     create_path: access_permissions_protocols_path(id: @protocol.id),
     assignable_path: edit_access_permissions_protocol_path(@protocol)
   },
diff --git a/app/views/access_permissions/protocols/show.json.jbuilder b/app/views/access_permissions/protocols/show.json.jbuilder
index faedde483..98ad6a7b3 100644
--- a/app/views/access_permissions/protocols/show.json.jbuilder
+++ b/app/views/access_permissions/protocols/show.json.jbuilder
@@ -1,12 +1,11 @@
 # frozen_string_literal: true
 
 json.modal controller.render_to_string(
-  partial: 'access_permissions/protocols/modals/show_modal',
+  partial: 'access_permissions/modals/show_modal',
   formats: [:html],
   locals: {
-    protocol: @protocol,
-    users: @protocol.assigned_users,
-    can_manage_resource: can_manage_protocol_users?(@protocol)
+    assignable: @protocol,
+    manually_assigned_users: @protocol.manually_assigned_users
   },
   layout: false
 )

From ca76c78a237cd8fba5658d05958fb5d6f3e7ceb9 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Mon, 6 Mar 2023 19:31:45 +0100
Subject: [PATCH 23/41] Fix protocol creation error message [SCI-8003]

---
 app/controllers/protocols_controller.rb | 2 +-
 config/locales/en.yml                   | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index bd5be2e73..1fa59ad59 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -300,7 +300,7 @@ class ProtocolsController < ApplicationController
       log_activity(:create_protocol_in_repository, nil, protocol: @protocol.id)
       redirect_to protocol_path(@protocol)
     else
-      render json: { error: @protocol.errors.full_messages.join(', ') }, status: :unprocessable_entity
+      render json: { error: @protocol.errors.messages.map { |_k, v| v }.join(', ') }, status: :unprocessable_entity
     end
   end
 
diff --git a/config/locales/en.yml b/config/locales/en.yml
index d1e67e82a..4501d1fdb 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -156,6 +156,8 @@ en:
           attributes:
             step_order:
               invalid: "Invalid step order."
+            name:
+              taken: "This protocol template name has to be unique inside a team (this includes the archive)."
         step:
           attributes:
             step_orderable_element_order:

From 4a02a130f05de8e34bb4e54610abab5aca1e6ab3 Mon Sep 17 00:00:00 2001
From: Giga Chubinidze <gchubinidze@unisens.ge>
Date: Mon, 6 Mar 2023 23:44:47 +0400
Subject: [PATCH 24/41] Archived protocol template navigation, icon, button
 [SCI-7954]

---
 app/javascript/vue/protocol/protocolMetadata.vue | 2 +-
 app/serializers/protocol_serializer.rb           | 2 +-
 app/views/protocols/show.html.erb                | 3 +++
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/protocol/protocolMetadata.vue b/app/javascript/vue/protocol/protocolMetadata.vue
index 6007cecd4..d73dbdf3b 100644
--- a/app/javascript/vue/protocol/protocolMetadata.vue
+++ b/app/javascript/vue/protocol/protocolMetadata.vue
@@ -17,7 +17,7 @@
           <span class="fas fa-print" aria-hidden="true"></span>
         </a>
         <button class="btn btn-light" @click="openVersionsModal">{{ i18n.t("protocols.header.versions") }}</button>
-        <button v-if="!protocol.attributes.published" @click="$emit('publish')" class="btn btn-primary">{{ i18n.t("protocols.header.publish") }}</button>
+        <button v-if="protocol.attributes.urls.publish_url" @click="$emit('publish')" class="btn btn-primary">{{ i18n.t("protocols.header.publish") }}</button>
         <button v-if="protocol.attributes.urls.save_as_draft_url" @click="saveAsdraft" class="btn btn-secondary">{{ i18n.t("protocols.header.save_as_draft") }}</button>
       </div>
     </div>
diff --git a/app/serializers/protocol_serializer.rb b/app/serializers/protocol_serializer.rb
index 9d36c3e46..38d0fd0d6 100644
--- a/app/serializers/protocol_serializer.rb
+++ b/app/serializers/protocol_serializer.rb
@@ -8,7 +8,7 @@ class ProtocolSerializer < ActiveModel::Serializer
 
   attributes :name, :id, :urls, :description, :description_view, :updated_at, :in_repository,
              :created_at_formatted, :updated_at_formatted, :added_by, :authors, :keywords, :version, :code,
-             :published, :version_comment
+             :published, :version_comment, :archived
 
   def updated_at
     object.updated_at.to_i
diff --git a/app/views/protocols/show.html.erb b/app/views/protocols/show.html.erb
index b79a31a3a..4110014fe 100644
--- a/app/views/protocols/show.html.erb
+++ b/app/views/protocols/show.html.erb
@@ -22,6 +22,9 @@
                         config: @inline_editable_title_config
                       } %>
         <% else %>
+          <% if @protocol.archived %>
+            <i class="fas fa-archive"></i>&nbsp;
+          <% end %>
           <div class="name-readonly-placeholder">
             <%= @protocol.name %>
           </div>

From 00c602a818820cc6af7e2aabd0ad7d9b8ff522fd Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 7 Mar 2023 09:42:18 +0100
Subject: [PATCH 25/41] Improve filtering in protocols datatable [SCI-8020]
 (#5068)

---
 app/datatables/protocols_datatable.rb | 72 ++++++++-------------------
 1 file changed, 21 insertions(+), 51 deletions(-)

diff --git a/app/datatables/protocols_datatable.rb b/app/datatables/protocols_datatable.rb
index 234bcdaa4..8bf19e8f6 100644
--- a/app/datatables/protocols_datatable.rb
+++ b/app/datatables/protocols_datatable.rb
@@ -54,8 +54,8 @@ class ProtocolsDatatable < CustomDatatable
   def as_json(_options = {})
     {
       draw: dt_params[:draw].to_i,
-      recordsTotal: get_raw_records.length,
-      recordsFiltered: filter_records(get_raw_records).length,
+      recordsTotal: get_raw_records_base.distinct.count,
+      recordsFiltered: records.present? ? records.first.filtered_count : 0,
       data: data
     }
   end
@@ -79,7 +79,7 @@ class ProtocolsDatatable < CustomDatatable
       casted_column = ::Arel::Nodes::NamedFunction.new('CAST',
                         [model.arel_table[column.to_sym].as(typecast)])
     end
-    casted_column.matches("%#{value}%")
+    casted_column.matches("%#{ActiveRecord::Base.sanitize_sql_like(value)}%")
   end
 
   private
@@ -108,6 +108,10 @@ class ProtocolsDatatable < CustomDatatable
     end
   end
 
+  def fetch_records
+    super.select('COUNT("protocols"."id") OVER() AS filtered_count')
+  end
+
   def filter_protocols_records(records)
     if params[:name_and_keywords].present?
       records = records.where_attributes_like(['protocols.name', 'protocol_keywords.name'], params[:name_and_keywords])
@@ -164,8 +168,16 @@ class ProtocolsDatatable < CustomDatatable
       "(#{new_drafts.to_sql}))"
     )
 
+    records = @type == :archived ? records.archived : records.active
+
+    records.with_granted_permissions(@user, ProtocolPermissions::READ)
+  end
+
+  # Query database for records (this will be later paginated and filtered)
+  # after that "data" function will return json
+  def get_raw_records
     records =
-      records
+      get_raw_records_base
       .preload(:parent, :latest_published_version, :draft, :protocol_keywords, user_assignments: %i(user user_role))
       .joins("LEFT OUTER JOIN protocols protocol_versions " \
              "ON protocol_versions.protocol_type = #{Protocol.protocol_types[:in_repository_published_version]} " \
@@ -174,26 +186,16 @@ class ProtocolsDatatable < CustomDatatable
              'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
       .joins('LEFT OUTER JOIN "protocol_keywords" ' \
              'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
-      .with_granted_permissions(@user, ProtocolPermissions::READ)
-
-    records = records.joins('LEFT OUTER JOIN "users" "archived_users"
-                             ON "archived_users"."id" = "protocols"."archived_by_id"')
-    records = records.joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
-
-    records = @type == :archived ? records.archived : records.active
+      .joins('LEFT OUTER JOIN "users" "archived_users" ON "archived_users"."id" = "protocols"."archived_by_id"')
+      .joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
+      .group('"protocols"."id"')
 
     records = filter_protocols_records(records)
-    records.group('"protocols"."id"')
-  end
-
-  # Query database for records (this will be later paginated and filtered)
-  # after that "data" function will return json
-  def get_raw_records
-    get_raw_records_base.select(
+    records.select(
       '"protocols".*',
       'COALESCE("protocols"."parent_id", "protocols"."id") AS adjusted_parent_id',
       'STRING_AGG(DISTINCT("protocol_keywords"."name"), \', \') AS "protocol_keywords_str"',
-      "CASE WHEN protocols.protocol_type = #{Protocol.protocol_types[:in_repository_draft]}" \
+      "CASE WHEN protocols.protocol_type = #{Protocol.protocol_types[:in_repository_draft]} " \
       "THEN COUNT(DISTINCT(\"protocol_versions\".\"id\")) ELSE COUNT(DISTINCT(\"protocol_versions\".\"id\")) + 1 " \
       "END AS nr_of_versions",
       'COUNT("user_assignments"."id") AS "nr_of_assigned_users"',
@@ -258,36 +260,4 @@ class ProtocolsDatatable < CustomDatatable
   def modified_timestamp(record)
     I18n.l(record.updated_at, format: :full)
   end
-
-  # OVERRIDE - This is only called when filtering results;
-  # when using GROUP BY function, SQL cannot perform a WHERE
-  # clause on aggregated columns (protocol keywords & users' full_name), but
-  # since we want those 2 columns to be searchable/filterable, we do an "inner"
-  # query where we select only protocol IDs which are filtered by those 2 columns
-  # using HAVING keyword (which is the correct way to filter aggregated columns).
-  # Another OR is then appended to the WHERE clause, checking if protocol is inside
-  # this list of IDs.
-  # def build_conditions_for(query)
-  #   # Inner query to retrieve list of protocol IDs where concatenated
-  #   # protocol keywords string, or user's full_name contains searched query
-  #   search_val = dt_params[:search][:value]
-  #   records_having = get_raw_records_base.having(
-  #     ::Arel::Nodes::NamedFunction.new(
-  #       'CAST',
-  #       [::Arel::Nodes::SqlLiteral.new("string_agg(\"protocol_keywords\".\"name\", ' ') AS #{typecast}")]
-  #     ).matches("%#{sanitize_sql_like(search_val)}%").to_sql +
-  #     " OR " +
-  #     ::Arel::Nodes::NamedFunction.new(
-  #       'CAST',
-  #       [::Arel::Nodes::SqlLiteral.new("max(\"users\".\"full_name\") AS #{typecast}")]
-  #     ).matches("%#{sanitize_sql_like(search_val)}%").to_sql
-  #   ).select(:id)
-
-  #   # Call parent function
-  #   criteria = super(query)
-
-  #   # Aight, now append another or
-  #   criteria = criteria.or(Protocol.arel_table[:id].in(records_having.arel))
-  #   criteria
-  # end
 end

From 0ab89db29c0066fdae95ce2d8e211e07dda77ca4 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 7 Mar 2023 09:49:21 +0100
Subject: [PATCH 26/41] Fix protocol Publish button behaviour after canceling
 of publish action [SCI-8068] (#5081)

---
 app/javascript/vue/protocol/container.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/protocol/container.vue b/app/javascript/vue/protocol/container.vue
index 0837baefc..5dcc2c1a6 100644
--- a/app/javascript/vue/protocol/container.vue
+++ b/app/javascript/vue/protocol/container.vue
@@ -158,7 +158,7 @@
     <PublishProtocol v-if="publishing"
       :protocol="protocol"
       @publish="publishProtocol"
-      @close="closePublishModal"
+      @cancel="closePublishModal"
     />
   </div>
 </template>

From 1d9785efbe9db34d8462fa3ea9a314056617fe15 Mon Sep 17 00:00:00 2001
From: aignatov-bio <47317017+aignatov-bio@users.noreply.github.com>
Date: Tue, 7 Mar 2023 09:52:31 +0100
Subject: [PATCH 27/41] Fix version button at action toolbar [SCI-8065] (#5085)

---
 app/assets/javascripts/protocols/index.js | 10 +++++++---
 app/datatables/protocols_datatable.rb     |  3 ++-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/app/assets/javascripts/protocols/index.js b/app/assets/javascripts/protocols/index.js
index c5f010e47..4ca717b0a 100644
--- a/app/assets/javascripts/protocols/index.js
+++ b/app/assets/javascripts/protocols/index.js
@@ -403,8 +403,8 @@ var ProtocolsIndex = (function() {
     let protocolsContainer = '.protocols-container';
     let versionsModal = '#protocol-versions-modal';
 
-    protocolsTableEl.on('click', '.protocol-versions-link', function(e) {
-      $.get(this.href, function(data) {
+    function loadVersionModal(href) {
+      $.get(href, function(data) {
         $(protocolsContainer).append($.parseHTML(data.html));
         $(versionsModal).modal('show');
         inlineEditing.init();
@@ -415,12 +415,16 @@ var ProtocolsIndex = (function() {
           $(versionsModal).remove();
         });
       });
+    }
+
+    protocolsTableEl.on('click', '.protocol-versions-link', function(e) {
+      loadVersionModal(this.href);
       e.stopPropagation();
       e.preventDefault();
     });
 
     $(protocolsContainer).on('click', '#protocolVersions', function() {
-      $(`tr[data-row-id=${rowsSelected[0]}] .protocol-versions-link`).click();
+      loadVersionModal($(`tr[data-row-id=${rowsSelected[0]}]`).data('versions-url'));
     });
   }
 
diff --git a/app/datatables/protocols_datatable.rb b/app/datatables/protocols_datatable.rb
index 8bf19e8f6..7b557e1bc 100644
--- a/app/datatables/protocols_datatable.rb
+++ b/app/datatables/protocols_datatable.rb
@@ -91,7 +91,8 @@ class ProtocolsDatatable < CustomDatatable
       {
         DT_RowId: record.id,
         DT_RowAttr: {
-          'data-permissions-url': permissions_protocol_path(parent)
+          'data-permissions-url': permissions_protocol_path(parent),
+          'data-versions-url': versions_modal_protocol_path(parent)
         },
         '1': name_html(parent),
         '2': parent.code,

From 8956d72f12be2e0b50104e0d54de3f63771c6797 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 7 Mar 2023 09:58:36 +0100
Subject: [PATCH 28/41] Switch to showing of total sum of all versions in
 protocols table [SCI-8066] (#5082)

---
 app/controllers/protocols_controller.rb |  6 +++---
 app/datatables/protocols_datatable.rb   | 21 +++++++++++++++++----
 app/models/protocol.rb                  |  1 +
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index bd5be2e73..61ee16442 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -410,7 +410,7 @@ class ProtocolsController < ApplicationController
       Protocol.transaction do
         begin
           @protocol.unlink
-        rescue Exception
+        rescue StandardError
           transaction_error = true
           raise ActiveRecord::Rollback
         end
@@ -769,9 +769,9 @@ class ProtocolsController < ApplicationController
       Protocol.transaction do
         begin
           protocol = @importer.import_new_protocol(@db_json)
-        rescue Exception
+        rescue StandardError
           transaction_error = true
-          raise ActiveRecord:: Rollback
+          raise ActiveRecord::Rollback
         end
       end
       p_name =
diff --git a/app/datatables/protocols_datatable.rb b/app/datatables/protocols_datatable.rb
index 7b557e1bc..a2d8635c7 100644
--- a/app/datatables/protocols_datatable.rb
+++ b/app/datatables/protocols_datatable.rb
@@ -30,7 +30,7 @@ class ProtocolsDatatable < CustomDatatable
       'adjusted_parent_id',
       'nr_of_versions',
       'protocol_keywords_str',
-      'nr_of_linked_children',
+      'nr_of_linked_tasks',
       'nr_of_assigned_users',
       'full_username_str',
       'published_on',
@@ -183,6 +183,16 @@ class ProtocolsDatatable < CustomDatatable
       .joins("LEFT OUTER JOIN protocols protocol_versions " \
              "ON protocol_versions.protocol_type = #{Protocol.protocol_types[:in_repository_published_version]} " \
              "AND protocol_versions.parent_id = protocols.parent_id")
+      .joins("LEFT OUTER JOIN protocols self_linked_task_protocols " \
+             "ON self_linked_task_protocols.protocol_type = #{Protocol.protocol_types[:linked]} " \
+             "AND self_linked_task_protocols.parent_id = protocols.id")
+      .joins("LEFT OUTER JOIN protocols parent_linked_task_protocols " \
+             "ON parent_linked_task_protocols.protocol_type = #{Protocol.protocol_types[:linked]} " \
+             "AND parent_linked_task_protocols.parent_id = protocols.parent_id")
+      .joins("LEFT OUTER JOIN protocols version_linked_task_protocols " \
+             "ON version_linked_task_protocols.protocol_type = #{Protocol.protocol_types[:linked]} " \
+             "AND version_linked_task_protocols.parent_id = protocol_versions.id " \
+             "AND version_linked_task_protocols.parent_id != protocols.id")
       .joins('LEFT OUTER JOIN "protocol_protocol_keywords" ' \
              'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
       .joins('LEFT OUTER JOIN "protocol_keywords" ' \
@@ -197,8 +207,11 @@ class ProtocolsDatatable < CustomDatatable
       'COALESCE("protocols"."parent_id", "protocols"."id") AS adjusted_parent_id',
       'STRING_AGG(DISTINCT("protocol_keywords"."name"), \', \') AS "protocol_keywords_str"',
       "CASE WHEN protocols.protocol_type = #{Protocol.protocol_types[:in_repository_draft]} " \
-      "THEN COUNT(DISTINCT(\"protocol_versions\".\"id\")) ELSE COUNT(DISTINCT(\"protocol_versions\".\"id\")) + 1 " \
+      "THEN 0 ELSE COUNT(DISTINCT(\"protocol_versions\".\"id\")) + 1 " \
       "END AS nr_of_versions",
+      '(COUNT(DISTINCT("self_linked_task_protocols"."id")) + ' \
+      'COUNT(DISTINCT("parent_linked_task_protocols"."id")) + ' \
+      'COUNT(DISTINCT("version_linked_task_protocols"."id"))) AS nr_of_linked_tasks',
       'COUNT("user_assignments"."id") AS "nr_of_assigned_users"',
       'MAX("users"."full_name") AS "full_username_str"', # "Hack" to get single username
       'MAX("archived_users"."full_name") AS "archived_full_username_str"'
@@ -232,8 +245,8 @@ class ProtocolsDatatable < CustomDatatable
 
   def modules_html(record)
     "<a href='#' data-action='load-linked-children'" \
-      "data-url='#{linked_children_protocol_path(record)}'>" \
-      "#{record.nr_of_linked_children}" \
+      "data-url='#{linked_children_protocol_path(record.parent || record)}'>" \
+      "#{record.nr_of_linked_tasks}" \
       "</a>"
   end
 
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 0cf60f09c..94a39c27b 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -123,6 +123,7 @@ class Protocol < ApplicationRecord
              class_name: 'User',
              inverse_of: :published_protocols, optional: true
   has_many :linked_children,
+           -> { linked },
            class_name: 'Protocol',
            foreign_key: 'parent_id'
   has_one  :next_version,

From 55dca41434b7fce24c96b3fa5e62e213fb588cd2 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 7 Mar 2023 10:44:44 +0100
Subject: [PATCH 29/41] Fix archive/restore propagation [SCI-8004]

---
 app/controllers/protocols_controller.rb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index bd5be2e73..6ef38b0d8 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -1107,10 +1107,12 @@ class ProtocolsController < ApplicationController
     begin
       Protocol.transaction do
         @protocols.find_each do |protocol|
+          protocol = protocol.parent if protocol.parent_id
           protocol.method(action).call(current_user)
         end
       end
-    rescue
+    rescue StandardError => e
+      Rails.logger.error e.message
       rollbacked = true
     end
 

From b9193748fa6b1ee29d5a3768f3e72922b5a1327b Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 7 Mar 2023 11:17:56 +0100
Subject: [PATCH 30/41] Fix view access modals [SCI-8040] (#5084)

---
 app/views/access_permissions/modals/_show_modal.html.erb  | 2 +-
 app/views/access_permissions/projects/show.json.jbuilder  | 3 +--
 app/views/access_permissions/protocols/show.json.jbuilder | 1 +
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/views/access_permissions/modals/_show_modal.html.erb b/app/views/access_permissions/modals/_show_modal.html.erb
index 5ca328499..769517e95 100644
--- a/app/views/access_permissions/modals/_show_modal.html.erb
+++ b/app/views/access_permissions/modals/_show_modal.html.erb
@@ -5,7 +5,7 @@
     <div class="modal-content" id="user_assignments_modal">
       <div class="modal-header">
         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-        <h4 class="modal-title"><%= t "access_permissions.#{assignable.class.name.pluralize.underscore}.modals.show_modal.title", resource_name: assignable.name %></h4>
+        <h4 class="modal-title"><%= t("access_permissions.#{assignable.class.name.pluralize.underscore}.modals.show_modal.title", resource_name: assignable.name) %></h4>
       </div>
       <div class="modal-body">
         <% manually_assigned_users.order(full_name: :asc).each do |user| %>
diff --git a/app/views/access_permissions/projects/show.json.jbuilder b/app/views/access_permissions/projects/show.json.jbuilder
index 67961114c..40744273a 100644
--- a/app/views/access_permissions/projects/show.json.jbuilder
+++ b/app/views/access_permissions/projects/show.json.jbuilder
@@ -6,8 +6,7 @@ json.modal controller.render_to_string(
   locals: {
     assignable: @project,
     manually_assigned_users: @project.manually_assigned_users,
-    top_level_assignable: @project,
-    users: @project.manually_assigned_users
+    top_level_assignable: @project
   },
   layout: false
 )
diff --git a/app/views/access_permissions/protocols/show.json.jbuilder b/app/views/access_permissions/protocols/show.json.jbuilder
index 98ad6a7b3..9353a07da 100644
--- a/app/views/access_permissions/protocols/show.json.jbuilder
+++ b/app/views/access_permissions/protocols/show.json.jbuilder
@@ -5,6 +5,7 @@ json.modal controller.render_to_string(
   formats: [:html],
   locals: {
     assignable: @protocol,
+    top_level_assignable: @protocol,
     manually_assigned_users: @protocol.manually_assigned_users
   },
   layout: false

From 25050cb6cc48ad2742972eab33fd2a7e3df79240 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 7 Mar 2023 11:25:59 +0100
Subject: [PATCH 31/41] Fix print protocol button on protocol show page
 [SCI-8079]

---
 app/javascript/vue/protocol/protocolMetadata.vue | 2 +-
 app/serializers/protocol_serializer.rb           | 9 ++++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/protocol/protocolMetadata.vue b/app/javascript/vue/protocol/protocolMetadata.vue
index 6007cecd4..466a22a1b 100644
--- a/app/javascript/vue/protocol/protocolMetadata.vue
+++ b/app/javascript/vue/protocol/protocolMetadata.vue
@@ -13,7 +13,7 @@
         </a>
       </div>
       <div class="actions-block">
-        <a class="btn btn-light icon-btn pull-right" data-toggle="modal" data-target="#print-protocol-modal" tabindex="0">
+        <a class="btn btn-light icon-btn pull-right" :href="protocol.attributes.urls.print_protocol_url" target="_blank">
           <span class="fas fa-print" aria-hidden="true"></span>
         </a>
         <button class="btn btn-light" @click="openVersionsModal">{{ i18n.t("protocols.header.versions") }}</button>
diff --git a/app/serializers/protocol_serializer.rb b/app/serializers/protocol_serializer.rb
index 9d36c3e46..d85dd63c8 100644
--- a/app/serializers/protocol_serializer.rb
+++ b/app/serializers/protocol_serializer.rb
@@ -75,7 +75,8 @@ class ProtocolSerializer < ActiveModel::Serializer
       delete_steps_url: delete_steps_url,
       publish_url: publish_url,
       save_as_draft_url: save_as_draft_url,
-      versions_modal_url: versions_modal_url
+      versions_modal_url: versions_modal_url,
+      print_protocol_url: print_protocol_url
     }
   end
 
@@ -115,6 +116,12 @@ class ProtocolSerializer < ActiveModel::Serializer
     versions_modal_protocol_path(object.parent || object)
   end
 
+  def print_protocol_url
+    return unless can_read_protocol_in_repository?(object)
+
+    print_protocol_path(object)
+  end
+
   def reorder_steps_url
     return unless can_manage_protocol_in_module?(object) || can_manage_protocol_in_repository?(object)
 

From ece09ee9a5d53e8e399356664cf191f19098b51d Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 7 Mar 2023 11:44:03 +0100
Subject: [PATCH 32/41] Add empty state for protocol actions toolbar [SCI-8077]

---
 app/assets/javascripts/protocols/index.js          | 2 ++
 app/assets/stylesheets/shared/datatable.scss       | 5 +++++
 app/views/protocols/index/_action_toolbar.html.erb | 3 +++
 config/locales/en.yml                              | 1 +
 4 files changed, 11 insertions(+)

diff --git a/app/assets/javascripts/protocols/index.js b/app/assets/javascripts/protocols/index.js
index 4ca717b0a..c018524d9 100644
--- a/app/assets/javascripts/protocols/index.js
+++ b/app/assets/javascripts/protocols/index.js
@@ -695,6 +695,8 @@ var ProtocolsIndex = (function() {
     actionToolbar.find('.btn').removeClass('btn-primary').addClass('btn-light');
     actionToolbar.find('.btn:visible').first().addClass('btn-primary').removeClass('btn-light');
     actionToolbar.find('.btn').removeClass('notransition');
+
+    actionToolbar.find('.emptyPlaceholder').toggleClass('hidden', actionToolbar.find('.btn:visible').length > 0);
   }
 
   /*
diff --git a/app/assets/stylesheets/shared/datatable.scss b/app/assets/stylesheets/shared/datatable.scss
index 6b5ea33c4..23968d2d1 100644
--- a/app/assets/stylesheets/shared/datatable.scss
+++ b/app/assets/stylesheets/shared/datatable.scss
@@ -56,6 +56,11 @@
       top: 0;
       width: 100%;
 
+      .emptyPlaceholder {
+        color: $color-volcano;
+        margin-left: 12px;
+      }
+
       .btn {
         margin-right: .25em;
       }
diff --git a/app/views/protocols/index/_action_toolbar.html.erb b/app/views/protocols/index/_action_toolbar.html.erb
index 3ac83ba6a..b990c8920 100644
--- a/app/views/protocols/index/_action_toolbar.html.erb
+++ b/app/views/protocols/index/_action_toolbar.html.erb
@@ -23,4 +23,7 @@
     <i class="fas fa-undo"></i>
     <span class="button-text"><%= t("protocols.index.action_toolbar.restore") %></span>
   </button>
+  <div class="emptyPlaceholder hidden">
+    <%= t("protocols.index.action_toolbar.empty_placeholder") %>
+  </div>
 </template>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 4501d1fdb..7a4a517aa 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -2720,6 +2720,7 @@ en:
         export: "Export"
         archive: "Archive"
         restore: "Restore"
+        empty_placeholder: "There is no action available"
       public_description: "Team protocols are visible and can be used by everyone from the team."
       private_description: "My protocols are only visible to you."
       create_new: "New protocol"

From 5e6f0fad83e9875de1fd3b02539ea9d5cf44d038 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 7 Mar 2023 12:14:02 +0100
Subject: [PATCH 33/41] Access modal translation amends [SCI-8060]

---
 config/locales/en.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 4501d1fdb..d53c33cb0 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -3218,9 +3218,9 @@ en:
 
   access_permissions:
     everyone_else: "Everyone else at %{team_name}"
-    reset: "The inherited role will be applied"
+    reset: "Inherit role"
     remove_access: "Remove access"
-    grant_access: "Grant access"
+    grant_access: "Grant new access"
     create:
       success:
         one: "You have successfully granted access to %{count} member to the project."
@@ -3235,15 +3235,15 @@ en:
         new_resource_assignments: "Grant new access to %{resource}"
       new_assignments_form:
         title: "Select members"
-        submit: "Grant access"
-        submit_singular: "Grant access to 1 user"
-        submit_plural: "Grant access to {num} users"
+        submit: "Grant new access"
+        submit_singular: "Grant access to 1 member"
+        submit_plural: "Grant access to {num} members"
         find_people_html: "Find people"
       new_protocol_assignments_form:
         title: "Select members"
-        submit: "Grant access"
-        submit_singular: "Grant access to 1 user"
-        submit_plural: "Grant access to {num} users"
+        submit: "Grant new access"
+        submit_singular: "Grant access to 1 member"
+        submit_plural: "Grant access to {num} members"
         find_people_html: "Find people"
       experiment_member_field:
         reset: "Inherit role"

From f8a4e7ee6535d6eaabdaf7642098366776435307 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 7 Mar 2023 13:03:01 +0100
Subject: [PATCH 34/41] Update logic for linked protocol templates with task
 [SCI-7973] (#5058)

---
 app/controllers/protocols_controller.rb       | 65 ---------------
 app/models/my_module.rb                       |  8 --
 app/models/protocol.rb                        | 83 +++++--------------
 app/serializers/protocol_serializer.rb        |  3 +-
 .../protocols/_protocol_status_bar.html.erb   |  4 +-
 config/locales/en.yml                         |  2 -
 spec/controllers/protocols_controller_spec.rb | 17 ----
 spec/factories/protocols.rb                   |  1 -
 .../model_importers/team_importer_spec.rb     |  3 -
 9 files changed, 23 insertions(+), 163 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index eb1eda20e..80c6110e7 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -49,10 +49,6 @@ class ProtocolsController < ApplicationController
     update_from_parent_modal
     delete_steps
   )
-  before_action :check_manage_parent_in_repository_permissions, only: %i(
-    update_parent
-    update_parent_modal
-  )
   before_action :check_manage_all_in_repository_permissions, only: :make_private
   before_action :check_restore_all_in_repository_permissions, only: :restore
   before_action :check_archive_all_in_repository_permissions, only: :archive
@@ -477,47 +473,6 @@ class ProtocolsController < ApplicationController
     end
   end
 
-  def update_parent
-    respond_to do |format|
-      if @protocol.parent.can_destroy?
-        transaction_error = false
-        Protocol.transaction do
-          @protocol.update_parent(current_user)
-        rescue StandardError
-          transaction_error = true
-          raise ActiveRecord::Rollback
-        end
-
-        if transaction_error
-          # Bad request error
-          format.json do
-            render json: {
-              message: t('my_modules.protocols.update_parent_error')
-            },
-            status: :bad_request
-          end
-        else
-          # Everything good, record activity, display flash & render 200
-          log_activity(:update_protocol_in_repository_from_task,
-                       @protocol.my_module.experiment.project,
-                       my_module: @protocol.my_module.id,
-                       protocol_repository: @protocol.parent.id)
-          flash[:success] = t(
-            'my_modules.protocols.update_parent_flash'
-          )
-          flash.keep(:success)
-          format.json { render json: {}, status: :ok }
-        end
-      else
-        format.json do
-          render json: {
-            message: t('my_modules.protocols.update_parent_error_locked')
-          }, status: :bad_request
-        end
-      end
-    end
-  end
-
   def update_from_parent
     protocol_can_destroy = @protocol.can_destroy?
     respond_to do |format|
@@ -912,19 +867,6 @@ class ProtocolsController < ApplicationController
     end
   end
 
-  def update_parent_modal
-    respond_to do |format|
-      format.json do
-        render json: {
-          title: t('my_modules.protocols.confirm_link_update_modal.update_parent_title'),
-          message: t('my_modules.protocols.confirm_link_update_modal.update_parent_message'),
-          btn_text: t('general.update'),
-          url: update_parent_protocol_path(@protocol)
-        }
-      end
-    end
-  end
-
   def update_from_parent_modal
     respond_to do |format|
       format.json do
@@ -1202,13 +1144,6 @@ class ProtocolsController < ApplicationController
                       can_delete_protocol_draft_in_repository?(@protocol)
   end
 
-  def check_manage_parent_in_repository_permissions
-    @protocol = Protocol.find_by_id(params[:id])
-    render_403 unless @protocol.present? &&
-                      can_read_protocol_in_module?(@protocol) &&
-                      can_manage_protocol_in_repository?(@protocol.parent)
-  end
-
   def check_manage_all_in_repository_permissions
     @protocols = Protocol.where(id: params[:protocol_ids])
     @protocols.find_each do |protocol|
diff --git a/app/models/my_module.rb b/app/models/my_module.rb
index ed883bf4e..829c21d9b 100644
--- a/app/models/my_module.rb
+++ b/app/models/my_module.rb
@@ -404,14 +404,6 @@ class MyModule < ApplicationRecord
     clone_tinymce_assets(target_my_module, target_my_module.experiment.project.team)
     target_my_module.protocols << protocol.deep_clone_my_module(self, current_user)
     target_my_module.reload
-
-    # fixes linked protocols
-    target_my_module.protocols.each do |protocol|
-      next unless protocol.linked?
-
-      protocol.updated_at = protocol.parent_updated_at
-      protocol.save
-    end
   end
 
   # Find an empty position for the restored module. It's
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 94a39c27b..dd252bc68 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -54,23 +54,22 @@ class Protocol < ApplicationRecord
     validate :linked_parent_type_constrain
     validates :added_by, presence: true
     validates :parent, presence: true
-    validates :parent_updated_at, presence: true
   end
   with_options if: :in_repository? do
     validates :name, presence: true
     validates :added_by, presence: true
     validates :my_module, absence: true
-    validates :parent_updated_at, absence: true
     validate :version_number_constraint
   end
   with_options if: :in_repository_published_version? do
     validates :parent, presence: true
-    validate :versions_same_name_constrain
+    validate :parent_type_constraint
+    validate :versions_same_name_constraint
   end
   with_options if: :in_repository_draft? do
     # Only one draft can exist for each protocol
     validate :ensure_single_draft
-    validate :versions_same_name_constrain
+    validate :versions_same_name_constraint
   end
   with_options if: -> { in_repository? && !parent } do |protocol|
     # Active protocol must have unique name inside its team
@@ -223,11 +222,8 @@ class Protocol < ApplicationRecord
   end
 
   def self.viewable_by_user(user, teams)
-    where(my_module: MyModule.viewable_by_user(user, teams))
-      .or(where(team: teams)
-            .where('protocol_type = 3 OR '\
-                   '(protocol_type = 2 AND added_by_id = :user_id)',
-                   user_id: user.id))
+    where(team: teams, protocol_type: REPOSITORY_TYPES).with_granted_permissions(user, ProtocolPermissions::READ)
+                                                       .or(where(my_module: MyModule.viewable_by_user(user, teams)))
   end
 
   def self.filter_by_teams(teams = [])
@@ -261,6 +257,16 @@ class Protocol < ApplicationRecord
     in_repository_draft? && parent.blank?
   end
 
+  def newer_published_version_present?
+    if in_repository_published_original?
+      published_versions.any?
+    elsif in_repository_published_version?
+      parent.published_versions.where('version_number > ?', version_number).any?
+    else
+      false
+    end
+  end
+
   def latest_published_version_or_self
     latest_published_version || self
   end
@@ -341,27 +347,12 @@ class Protocol < ApplicationRecord
     unlinked? || linked?
   end
 
-  def linked_no_diff?
-    linked? &&
-      updated_at == parent_updated_at &&
-      parent.updated_at == parent_updated_at
-  end
-
   def newer_than_parent?
-    linked? && parent.updated_at == parent_updated_at &&
-      updated_at > parent_updated_at
+    linked? && updated_at > parent.published_on
   end
 
   def parent_newer?
-    linked? &&
-      updated_at == parent_updated_at &&
-      parent.updated_at > parent_updated_at
-  end
-
-  def parent_and_self_newer?
-    linked? &&
-      parent.updated_at > parent_updated_at &&
-      updated_at > parent_updated_at
+    linked? && parent.newer_published_version_present?
   end
 
   def number_of_steps
@@ -385,9 +376,6 @@ class Protocol < ApplicationRecord
   end
 
   def make_private(user)
-    # Don't update "updated_at" timestamp
-    self.record_timestamps = false
-
     self.added_by = user
     self.published_on = nil
     self.archived_by = nil
@@ -488,8 +476,6 @@ class Protocol < ApplicationRecord
     result = true
     begin
       Protocol.transaction do
-        self.record_timestamps = false
-
         # First, destroy all keywords
         protocol_protocol_keywords.destroy_all
         if keywords.present?
@@ -508,31 +494,11 @@ class Protocol < ApplicationRecord
 
   def unlink
     self.parent = nil
-    self.parent_updated_at = nil
+    self.linked_at = nil
     self.protocol_type = Protocol.protocol_types[:unlinked]
     save!
   end
 
-  def update_parent(current_user)
-    ActiveRecord::Base.no_touching do
-      # First, destroy parent's step contents
-      parent.destroy_contents
-      parent.reload
-
-      # Now, clone step contents
-      Protocol.clone_contents(self, parent, current_user, false)
-    end
-
-    # Lastly, update the metadata
-    parent.reload
-    parent.record_timestamps = false
-    parent.updated_at = updated_at
-    parent.save!
-    self.record_timestamps = false
-    self.parent_updated_at = updated_at
-    save!
-  end
-
   def update_from_parent(current_user, source)
     ActiveRecord::Base.no_touching do
       # First, destroy step contents
@@ -546,7 +512,6 @@ class Protocol < ApplicationRecord
     reload
     self.record_timestamps = false
     self.updated_at = source.published_on
-    self.parent_updated_at = source.published_on
     self.added_by = current_user
     self.last_modified_by = current_user
     self.parent = source
@@ -569,7 +534,6 @@ class Protocol < ApplicationRecord
     self.record_timestamps = false
     self.updated_at = source.published_on
     self.parent = source
-    self.parent_updated_at = source.published_on
     self.added_by = current_user
     self.last_modified_by = current_user
     self.linked_at = Time.zone.now
@@ -627,7 +591,6 @@ class Protocol < ApplicationRecord
     if linked?
       clone.added_by = current_user
       clone.parent = parent
-      clone.parent_updated_at = parent_updated_at
     end
 
     deep_clone(clone, current_user)
@@ -804,19 +767,13 @@ class Protocol < ApplicationRecord
     end
   end
 
-  def version_parent_type_constrain
+  def parent_type_constraint
     unless parent.in_repository_published_original?
       errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_parent_type'))
     end
   end
 
-  def draft_parent_type_constrain
-    unless parent.in_repository_published_original?
-      errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_parent_type'))
-    end
-  end
-
-  def versions_same_name_constrain
+  def versions_same_name_constraint
     if parent.present? && !parent.name.eql?(name)
       errors.add(:base, I18n.t('activerecord.errors.models.protocol.wrong_version_name'))
     end
diff --git a/app/serializers/protocol_serializer.rb b/app/serializers/protocol_serializer.rb
index 38d0fd0d6..e8350eed2 100644
--- a/app/serializers/protocol_serializer.rb
+++ b/app/serializers/protocol_serializer.rb
@@ -140,8 +140,7 @@ class ProtocolSerializer < ActiveModel::Serializer
   end
 
   def update_protocol_url
-    return unless can_read_protocol_in_module?(object) && object.linked? &&
-                  (object.parent_newer? || object.parent_and_self_newer?)
+    return unless can_read_protocol_in_module?(object) && object.linked? && object.parent_newer?
 
     update_from_parent_modal_protocol_path(object, format: :json)
   end
diff --git a/app/views/my_modules/protocols/_protocol_status_bar.html.erb b/app/views/my_modules/protocols/_protocol_status_bar.html.erb
index a933316e0..1cb450313 100644
--- a/app/views/my_modules/protocols/_protocol_status_bar.html.erb
+++ b/app/views/my_modules/protocols/_protocol_status_bar.html.erb
@@ -9,7 +9,7 @@
     </span>
   <% end %>
   <a href="#" id="my-module-protocol-info-button" class="status-info
-    <%= 'parent-newer' if @protocol.parent_newer? || @protocol.parent_and_self_newer? %>
+    <%= 'parent-newer' if @protocol.parent_newer? %>
     <%= 'protocol-newer' if @protocol.newer_than_parent? %>
     " data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
     <i class="fas fa-info-circle"></i>
@@ -47,7 +47,7 @@
           <div class="value"><%= I18n.l(@protocol&.parent&.published_on, format: :full) %></div>
         </div>
         <div class="dropdown-footer">
-          <% if @protocol.parent_newer? || @protocol.parent_and_self_newer? %>
+          <% if @protocol.parent_newer? %>
             <div class="notification-line new-parent-version">
               <i class="fas fa-info-circle"></i>
               <div class="description"><%= t("my_modules.protocols.protocol_status_bar.messages.template_updated_html") %></div>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index f152fb947..30a165935 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1087,8 +1087,6 @@ en:
         revert_title: "Revert protocol template"
         revert_message: "This will override any changes you made. We can’t recover them once you revert."
         revert_btn_text: "Yes, revert it"
-        update_parent_title: "Update templates version"
-        update_parent_message: "Are you sure you want to update the templates protocol with this version? This will override any other changes made in the templates version."
         update_self_title: "Update from protocol templates"
         update_self_message: "This will override any changes you made. We can’t recover them once you update this protocol with the new version."
         update_self_btn_text: "Yes, update it"
diff --git a/spec/controllers/protocols_controller_spec.rb b/spec/controllers/protocols_controller_spec.rb
index c8284d769..25b4e2139 100644
--- a/spec/controllers/protocols_controller_spec.rb
+++ b/spec/controllers/protocols_controller_spec.rb
@@ -180,23 +180,6 @@ describe ProtocolsController, type: :controller do
           .to(change { Activity.count })
       end
     end
-
-    describe 'POST update_parent' do
-      let(:action) { put :update_parent, params: params, format: :json }
-
-      it 'calls create activity for updating protocol in repository from task' do
-        expect(Activities::CreateActivityService)
-          .to(receive(:call)
-                .with(hash_including(activity_type:
-                                       :update_protocol_in_repository_from_task)))
-        action
-      end
-
-      it 'adds activity in DB' do
-        expect { action }
-          .to(change { Activity.count })
-      end
-    end
   end
 
   describe 'POST load_from_repository' do
diff --git a/spec/factories/protocols.rb b/spec/factories/protocols.rb
index e13a77802..eef9af1af 100644
--- a/spec/factories/protocols.rb
+++ b/spec/factories/protocols.rb
@@ -15,7 +15,6 @@ FactoryBot.define do
       protocol_type { :linked }
       parent { create :protocol }
       added_by { create :user }
-      parent_updated_at { Time.now }
     end
   end
 end
diff --git a/spec/services/model_importers/team_importer_spec.rb b/spec/services/model_importers/team_importer_spec.rb
index 702ac79e6..6b8a9b349 100644
--- a/spec/services/model_importers/team_importer_spec.rb
+++ b/spec/services/model_importers/team_importer_spec.rb
@@ -187,9 +187,6 @@ describe TeamImporter do
             expect(db_protocol.restored_on).to be_nil
             expect(db_protocol.authors).to eq json_protocol['authors']
             expect(db_protocol.parent_id).to eq json_protocol['parent_id']
-            expect(db_protocol.parent_updated_at).to eq(
-              json_protocol['parent_updated_at']
-            )
             expect(db_protocol.protocol_type).to eq(
               json_protocol['protocol_type']
             )

From 22c039fc77d2b74087a4235bac9617dc7436d69d Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 7 Mar 2023 14:04:05 +0100
Subject: [PATCH 35/41] PET access modal fixes [SCI-8038]

---
 .../access_permissions/access_modal.scss      |  9 ++++
 .../access_permissions/projects_controller.rb |  2 +-
 .../my_modules/my_module_member.json.jbuilder |  2 +-
 .../_default_public_user_role_form.html.erb   | 52 +++++++++++--------
 4 files changed, 41 insertions(+), 24 deletions(-)

diff --git a/app/assets/stylesheets/access_permissions/access_modal.scss b/app/assets/stylesheets/access_permissions/access_modal.scss
index d83980af2..20b2b333a 100644
--- a/app/assets/stylesheets/access_permissions/access_modal.scss
+++ b/app/assets/stylesheets/access_permissions/access_modal.scss
@@ -10,6 +10,15 @@
     &:focus {
       box-shadow: none;
     }
+
+    &.disabled {
+      color: $color-black;
+      opacity: 1;
+
+      .caret {
+        opacity: 0;
+      }
+    }
   }
 
   .modal-body {
diff --git a/app/controllers/access_permissions/projects_controller.rb b/app/controllers/access_permissions/projects_controller.rb
index 57ae09775..4f55863c0 100644
--- a/app/controllers/access_permissions/projects_controller.rb
+++ b/app/controllers/access_permissions/projects_controller.rb
@@ -38,7 +38,7 @@ module AccessPermissions
       @user_assignment.update!(permitted_update_params)
 
       log_activity(:change_user_role_on_project, @user_assignment)
-      propagate_job(user_assignment)
+      propagate_job(@user_assignment)
 
       respond_to do |format|
         format.json do
diff --git a/app/views/access_permissions/my_modules/my_module_member.json.jbuilder b/app/views/access_permissions/my_modules/my_module_member.json.jbuilder
index a250dbeae..43b413999 100644
--- a/app/views/access_permissions/my_modules/my_module_member.json.jbuilder
+++ b/app/views/access_permissions/my_modules/my_module_member.json.jbuilder
@@ -5,7 +5,7 @@ json.form controller.render_to_string(
   formats: [:html],
   locals: {
     user: @user_assignment.user,
-    update_path: access_permissions_my_module_path(@my_module)
+    update_path: access_permissions_my_module_path(@my_module),
     with_inherit: true,
     assignable: @my_module
   },
diff --git a/app/views/access_permissions/partials/_default_public_user_role_form.html.erb b/app/views/access_permissions/partials/_default_public_user_role_form.html.erb
index 2fa1254ec..e6aa3dac8 100644
--- a/app/views/access_permissions/partials/_default_public_user_role_form.html.erb
+++ b/app/views/access_permissions/partials/_default_public_user_role_form.html.erb
@@ -1,3 +1,4 @@
+<% editable ||= false %>
 <% if assignable.visible? %>
   <%= form_with(model: assignable, url: [:update_default_public_user_role, :access_permissions, assignable], method: :put, remote: true, html: { class: 'member-item', id: 'public_assignments', data: { action: 'replace-form autosave-form', object_type: assignable.class.name.underscore.to_sym } }) do |f| %>
     <div class="user-assignment-info">
@@ -13,28 +14,35 @@
       <div class="user-assignment-role">
         <div class="user-assignment-controls">
           <div class="dropdown pull-right">
-            <button class="btn btn-light btn-role-select" type="button" id="defaultPublicUserRole" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
-              <%= f.object.default_public_user_role.name %>
-              <span class="caret"></span>
-            </button>
-            <%= f.hidden_field :default_public_user_role_id, value: f.object.default_public_user_role.id, class: "default-public-user-role-id" %>
-            <ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="defaultPublicUserRole">
-              <% user_roles_collection.each do |role| %>
-                <li>
-                  <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
-                    <%= role[0] %>
-                  </a>
-                </li>
-              <% end %>
-              <% if assignable.top_level_assignable?  %>
-                <li role="separator" class="divider" data-hook="support-dropdown-separator"></li>
-                <li>
-                  <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="">
-                    <%= t('access_permissions.remove_access') %>
-                  </a>
-                </li>
-              <% end %>
-            </ul>
+            <% if editable %>
+              <button class="btn btn-light btn-role-select" type="button" id="defaultPublicUserRole" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
+                <%= f.object.default_public_user_role.name %>
+                <span class="caret"></span>
+              </button>
+              <%= f.hidden_field :default_public_user_role_id, value: f.object.default_public_user_role.id, class: "default-public-user-role-id" %>
+              <ul class="dropdown-menu dropdown-menu-right user-assignment-dropdown" aria-labelledby="defaultPublicUserRole">
+                <% user_roles_collection.each do |role| %>
+                  <li>
+                    <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="<%= role[1] %>">
+                      <%= role[0] %>
+                    </a>
+                  </li>
+                <% end %>
+                <% if assignable.top_level_assignable?  %>
+                  <li role="separator" class="divider" data-hook="support-dropdown-separator"></li>
+                  <li>
+                    <a href="#" data-turbolinks="false" class="user-role-selector" data-role-id="">
+                      <%= t('access_permissions.remove_access') %>
+                    </a>
+                  </li>
+                <% end %>
+              </ul>
+            <% else %>
+              <button class="btn btn-light btn-role-select disabled" type="button">
+                <%= f.object.default_public_user_role.name %>
+                <span class="caret"></span>
+              </button>
+            <% end %>
           </div>
         </div>
       </div>

From bee0fa2de95d34f5e173fe39916ebef5a9095f81 Mon Sep 17 00:00:00 2001
From: Alex Kriuchykhin <oleksii@scinote.net>
Date: Tue, 7 Mar 2023 14:15:49 +0100
Subject: [PATCH 36/41] Fix protocols re-assigning when removing user from a
 team [SCI-8034] (#5069)

---
 app/controllers/users/settings/user_teams_controller.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/controllers/users/settings/user_teams_controller.rb b/app/controllers/users/settings/user_teams_controller.rb
index 8aed9996d..0300ff355 100644
--- a/app/controllers/users/settings/user_teams_controller.rb
+++ b/app/controllers/users/settings/user_teams_controller.rb
@@ -193,9 +193,9 @@ module Users
         Protocol.where(id: p_ids).find_each do |protocol|
           protocol.record_timestamps = false
           protocol.added_by = new_owner
-          protocol.archived_by = new_owner unless protocol.archived_by.nil?
-          protocol.restored_by = new_owner unless protocol.restored_by.nil?
-          protocol.save!
+          protocol.archived_by = new_owner if protocol.archived_by == user_assignment.user
+          protocol.restored_by = new_owner if protocol.restored_by == user_assignment.user
+          protocol.save!(validate: false)
           protocol.user_assignments.find_by(user: new_owner)&.destroy!
           protocol.user_assignments.create!(user: new_owner, user_role: UserRole.find_predefined_owner_role)
         end

From 078f4583ec18aa3062d95c26fe6702ee37c7c9e2 Mon Sep 17 00:00:00 2001
From: ajugo <andrej.jugovic7@gmail.com>
Date: Tue, 7 Mar 2023 14:19:29 +0100
Subject: [PATCH 37/41] Fix content of the Load from templates table [SCI-8049]
 (#5088)

---
 ...oad_from_repository_protocols_datatable.rb | 145 ++++++++----------
 1 file changed, 65 insertions(+), 80 deletions(-)

diff --git a/app/datatables/load_from_repository_protocols_datatable.rb b/app/datatables/load_from_repository_protocols_datatable.rb
index 88e1e4ed8..da8f7bd55 100644
--- a/app/datatables/load_from_repository_protocols_datatable.rb
+++ b/app/datatables/load_from_repository_protocols_datatable.rb
@@ -3,6 +3,8 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
   include ActiveRecord::Sanitization::ClassMethods
   include InputSanitizeHelper
 
+  PREFIXED_ID_SQL = "('#{Protocol::ID_PREFIX}' || COALESCE(\"protocols\".\"parent_id\", \"protocols\".\"id\"))".freeze
+
   def initialize(view, team, user)
     super(view)
     @team = team
@@ -12,8 +14,8 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
   def sortable_columns
     @sortable_columns ||= [
       'Protocol.name',
-      'nr_of_versions',
-      'Protocol.id',
+      'Protocol.version_number',
+      'adjusted_parent_id',
       'protocol_keywords_str',
       'full_username_str',
       'Protocol.published_on'
@@ -23,20 +25,18 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
   def searchable_columns
     @searchable_columns ||= [
       'Protocol.name',
-      'Protocol.id',
-      'Protocol.published_on'
+      "Protocol.#{PREFIXED_ID_SQL}",
+      'Protocol.published_on',
+      'Protocol.version_number',
+      'ProtocolKeyword.name'
     ]
   end
 
-  # This hack is needed to display a correct amount of
-  # searched entries (needed for pagination).
-  # This is needed because of usage of GROUP operator in SQL.
-  # See https://github.com/antillas21/ajax-datatables-rails/issues/112
-  def as_json(options = {})
+  def as_json(_options = {})
     {
       draw: dt_params[:draw].to_i,
-      recordsTotal: get_raw_records.length,
-      recordsFiltered: filter_records(get_raw_records).length,
+      recordsTotal: get_raw_records_base.distinct.count,
+      recordsFiltered: records.present? ? records.first.filtered_count : 0,
       data: data
     }
   end
@@ -46,33 +46,55 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
   # Returns json of current protocols (already paginated)
   def data
     records.map do |record|
+      parent = record.parent || record
       {
-        'DT_RowId': record.id,
+        DT_RowId: parent.id,
         '0': escape_input(record.name),
-        '1': record.nr_of_versions,
-        '2': record.code,
+        '1': record.version_number,
+        '2': parent.code,
         '3': keywords_html(record),
-        '4': escape_input(record.full_username_str),
+        '4': escape_input(record.published_by.full_name),
         '5': I18n.l(record.published_on, format: :full)
       }
     end
   end
 
-  def get_raw_records_base
-    records =
-      Protocol
-      .where(team: @team)
-      .where(protocols: { protocol_type: Protocol.protocol_types[:in_repository_published_original] })
-      .joins("LEFT OUTER JOIN protocols protocol_versions "\
-             "ON protocol_versions.protocol_type = #{Protocol.protocol_types[:in_repository_published_version]} "\
-             "AND protocol_versions.parent_id = protocols.id")
-      .joins('LEFT OUTER JOIN "protocol_protocol_keywords" '\
-             'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
-      .joins('LEFT OUTER JOIN "protocol_keywords"'\
-             'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
-      .joins('LEFT OUTER JOIN users ON users.id = protocols.published_by_id').active
+  def new_search_condition(column, value)
+    model, column = column.split('.', 2)
+    model = model.constantize
 
-    records.group('"protocols"."id"')
+    casted_column = case column
+                    when PREFIXED_ID_SQL
+                      ::Arel::Nodes::SqlLiteral.new(PREFIXED_ID_SQL)
+                    when 'published_on'
+                      ::Arel::Nodes::NamedFunction.new(
+                        'CAST', [Arel.sql("to_char( protocols.published_on, '#{formated_date}' ) AS VARCHAR")]
+                      )
+                    else
+                      ::Arel::Nodes::NamedFunction.new('CAST', [model.arel_table[column.to_sym].as(typecast)])
+                    end
+    casted_column.matches("%#{ActiveRecord::Base.sanitize_sql_like(value)}%")
+  end
+
+  def fetch_records
+    super.select('COUNT("protocols"."id") OVER() AS filtered_count')
+  end
+
+  def get_raw_records_base
+    original_without_versions = @team.protocols
+                                     .left_outer_joins(:published_versions)
+                                     .where(protocol_type: Protocol.protocol_types[:in_repository_published_original])
+                                     .where(published_versions: { id: nil })
+                                     .select(:id)
+
+    published_versions = @team.protocols
+                              .where(protocol_type: Protocol.protocol_types[:in_repository_published_version])
+                              .order('parent_id, version_number DESC')
+                              .select('DISTINCT ON (parent_id) id')
+
+    Protocol.where("protocols.id IN ((#{original_without_versions.to_sql}) UNION (#{published_versions.to_sql}))")
+            .active
+            .with_granted_permissions(@user, ProtocolPermissions::READ)
   end
 
   # OVERRIDE - query database for records (this will be
@@ -80,10 +102,17 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
   # will return json
   def get_raw_records
     get_raw_records_base
+      .preload(:parent, :protocol_keywords, user_assignments: %i(user user_role))
+      .joins('LEFT OUTER JOIN "protocol_protocol_keywords" ' \
+             'ON "protocol_protocol_keywords"."protocol_id" = "protocols"."id"')
+      .joins('LEFT OUTER JOIN "protocol_keywords" ' \
+             'ON "protocol_protocol_keywords"."protocol_keyword_id" = "protocol_keywords"."id"')
+      .joins('LEFT OUTER JOIN "users" ON "users"."id" = "protocols"."published_by_id"')
+      .group('"protocols"."id"')
       .select(
         '"protocols".*',
-        'STRING_AGG("protocol_keywords"."name", \', \') AS "protocol_keywords_str"',
-        'COUNT("protocol_versions"."id") + 1 AS "nr_of_versions"',
+        'COALESCE("protocols"."parent_id", "protocols"."id") AS adjusted_parent_id',
+        'STRING_AGG(DISTINCT("protocol_keywords"."name"), \', \') AS "protocol_keywords_str"',
         'MAX("users"."full_name") AS "full_username_str"'
       )
   end
@@ -91,59 +120,15 @@ class LoadFromRepositoryProtocolsDatatable < CustomDatatable
   # Various helper methods
 
   def keywords_html(record)
-    if record.protocol_keywords_str.blank?
+    if record.protocol_keywords.blank?
       "<i>#{I18n.t('protocols.no_keywords')}</i>"
     else
-      kws = record.protocol_keywords_str.split(', ')
       res = []
-      kws.sort_by(&:downcase).each do |kw|
-        res << "<a href='#' data-action='filter' data-param='#{kw}'>#{kw}</a>"
+      record.protocol_keywords.sort_by { |kw| kw.name.downcase }.each do |kw|
+        sanitized_kw = sanitize_input(kw.name)
+        res << "<a href='#' data-action='filter' data-param='#{sanitized_kw}'>#{sanitized_kw}</a>"
       end
-      sanitize_input(res.join(', '))
+      res.join(', ')
     end
   end
-
-  def timestamp_column_html(record)
-    if @type == :public
-      I18n.l(record.published_on, format: :full)
-    else
-      I18n.l(record.created_at, format: :full)
-    end
-  end
-
-  # OVERRIDE - This is only called when filtering results;
-  # when using GROUP BY function, SQL cannot perform a WHERE
-  # clause on aggregated columns (protocol keywords & users' full_name), but
-  # since we want those 2 columns to be searchable/filterable, we do an "inner"
-  # query where we select only protocol IDs which are filtered by those 2 columns
-  # using HAVING keyword (which is the correct way to filter aggregated columns).
-  # Another OR is then appended to the WHERE clause, checking if protocol is inside
-  # this list of IDs.
-  def build_conditions_for(query)
-    # Inner query to retrieve list of protocol IDs where concatenated
-    # protocol keywords string, or user's full_name contains searched query
-    search_val = dt_params[:search][:value]
-    records_having = get_raw_records_base.having(
-      ::Arel::Nodes::NamedFunction.new(
-        'CAST',
-        [::Arel::Nodes::SqlLiteral.new("string_agg(\"protocol_keywords\".\"name\", ' ') AS #{typecast}")]
-      ).matches("%#{sanitize_sql_like(search_val)}%").to_sql +
-      ' OR ' +
-      ::Arel::Nodes::NamedFunction.new(
-        'CAST',
-        [::Arel::Nodes::SqlLiteral.new("max(\"users\".\"full_name\") AS #{typecast}")]
-      ).matches("%#{sanitize_sql_like(search_val)}%").to_sql +
-      ' OR ' +
-      ::Arel::Nodes::NamedFunction.new(
-        'CAST',
-        [::Arel::Nodes::SqlLiteral.new("COUNT(\"protocol_versions\".\"id\") + 1 AS #{typecast}")]
-      ).matches("%#{sanitize_sql_like(search_val)}%").to_sql
-    ).select(:id)
-
-    # Call parent function
-    criteria = super(query)
-
-    # Aight, now append another or
-    criteria.or(Protocol.arel_table[:id].in(records_having.arel))
-  end
 end

From 2a794b68ac8edde9267dc4a56871f8a9a792d1a2 Mon Sep 17 00:00:00 2001
From: Anton <anton@scinote.net>
Date: Tue, 7 Mar 2023 14:31:15 +0100
Subject: [PATCH 38/41] Fix protocol duplication table reload [SCI-8074]

---
 app/assets/javascripts/protocols/index.js | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/app/assets/javascripts/protocols/index.js b/app/assets/javascripts/protocols/index.js
index c018524d9..540193f1d 100644
--- a/app/assets/javascripts/protocols/index.js
+++ b/app/assets/javascripts/protocols/index.js
@@ -516,13 +516,12 @@ var ProtocolsIndex = (function() {
         url: $el.data('url'),
         data: JSON.stringify({ ids: rowsSelected }),
         contentType: 'application/json'
-      },
-      (data) => {
-        animateSpinner(null, false);
-        HelperModule.flashAlertMsg(data.message, 'success');
-        reloadTable();
       }
-    ).error((data) => {
+    ).success((data) => {
+      animateSpinner(null, false);
+      HelperModule.flashAlertMsg(data.message, 'success');
+      reloadTable();
+    }).error((data) => {
       animateSpinner(null, false);
       HelperModule.flashAlertMsg(data.responseJSON.message, 'danger');
     });

From e4e8997cc17a8c530d52ba13ece3dae1ee49eed2 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 7 Mar 2023 14:45:52 +0100
Subject: [PATCH 39/41] Add draft created activity [SCI-8093]

---
 app/controllers/protocols_controller.rb | 1 +
 config/initializers/extends.rb          | 5 +++--
 config/locales/global_activities/en.yml | 1 +
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/app/controllers/protocols_controller.rb b/app/controllers/protocols_controller.rb
index 80c6110e7..14a65cbbe 100644
--- a/app/controllers/protocols_controller.rb
+++ b/app/controllers/protocols_controller.rb
@@ -389,6 +389,7 @@ class ProtocolsController < ApplicationController
         flash[:error] = draft.errors.full_messages.join(', ')
         redirect_to protocols_path
       else
+        log_activity(:protocol_template_draft_created, nil, protocol: @protocol.id)
         redirect_to protocol_path(draft)
       end
     rescue StandardError => e
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index 57a76f7de..9fe1a9b15 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -436,7 +436,8 @@ class Extends
     protocol_template_access_granted: 233,
     protocol_template_access_changed: 234,
     protocol_template_access_revoked: 235,
-    task_protocol_save_to_template: 236
+    task_protocol_save_to_template: 236,
+    protocol_template_draft_created: 237
   }
 
   ACTIVITY_GROUPS = {
@@ -453,7 +454,7 @@ class Extends
                   78, 96, 107, 113, 114, *133..136, 180, 181, 182],
     protocol_repository: [80, 103, 89, 87, 79, 90, 91, 88, 85, 86, 84, 81, 82,
                           83, 101, 112, 123, 125, 117, 119, 129, 131, 170, 173, 179, 187, 186,
-                          190, 191, *204..215, 220, 221, 223, 227, 228, 229, *230..235],
+                          190, 191, *204..215, 220, 221, 223, 227, 228, 229, *230..235, 237],
     team: [92, 94, 93, 97, 104],
     label_repository: [*216..219]
   }
diff --git a/config/locales/global_activities/en.yml b/config/locales/global_activities/en.yml
index a87d291fc..03ff2dc05 100644
--- a/config/locales/global_activities/en.yml
+++ b/config/locales/global_activities/en.yml
@@ -257,6 +257,7 @@ en:
       protocol_template_published_html: "%{user} published protocol template %{protocol} version %{version_number}"
       protocol_template_revision_notes_updated_html: "%{user} edited revision notes of %{protocol}"
       protocol_template_draft_deleted_html: "%{user} deleted draft of %{protocol}"
+      protocol_template_draft_created_html: "%{user} created draft of %{protocol}"
       protocol_template_access_granted_html: "%{user} granted access to %{user_target} with user role %{role} to protocol template %{protocol}"
       protocol_template_access_changed_html: "%{user} changed %{user_target}’s role on protocol template %{protocol} to %{role}"
       protocol_template_access_revoked_html: "%{user} removed %{user_target} with user role %{role} from protocol template %{protocol}"

From 6cc78790b0a0867043c5edcc1f9b9e3af9d346b7 Mon Sep 17 00:00:00 2001
From: Martin Artnik <martin@scinote.net>
Date: Tue, 7 Mar 2023 14:55:11 +0100
Subject: [PATCH 40/41] Fix title for archived protocols table [SCI-8092]

---
 app/views/protocols/index.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/protocols/index.html.erb b/app/views/protocols/index.html.erb
index d17973da1..21c15c58f 100644
--- a/app/views/protocols/index.html.erb
+++ b/app/views/protocols/index.html.erb
@@ -14,7 +14,7 @@
   <div class="content-pane flexible protocols-index <%= @type %>">
     <div class="content-header sticky-header">
       <div class="title-row">
-        <% if templates_view_mode_archived? %>
+        <% if templates_view_mode_archived?(type: @type) %>
           <h1>
             <i class="fas fa-archive"></i>
             <%= t('protocols.index.head_title_archived') %>

From a503aa1a9f072d5718670c2e8b97212404a0634e Mon Sep 17 00:00:00 2001
From: artoscinote <85488244+artoscinote@users.noreply.github.com>
Date: Wed, 8 Mar 2023 10:25:11 +0100
Subject: [PATCH 41/41] Add create draft activity name [SCI-8093]

---
 config/locales/global_activities/en.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/locales/global_activities/en.yml b/config/locales/global_activities/en.yml
index 03ff2dc05..01585c59a 100644
--- a/config/locales/global_activities/en.yml
+++ b/config/locales/global_activities/en.yml
@@ -473,6 +473,7 @@ en:
       protocol_template_published: "Protocol template published"
       protocol_template_revision_notes_updated: "Revision notes edited"
       protocol_template_draft_deleted: "Deleting draft"
+      protocol_template_draft_created: "Creating draft"
       protocol_template_access_granted: "User granted access to protocol template"
       protocol_template_access_changed: "User role changed on a protocol"
       protocol_template_access_revoked: "User removed from a protocol"