From 1ad8c259d1d18e6aa709538122b8ada3ebfe63cf Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Tue, 20 Mar 2018 14:45:57 +0100
Subject: [PATCH 01/23] add blank page for repositories [fixes SCI-2139]

---
 app/assets/javascripts/repositories/index.js |  74 +---------
 app/assets/javascripts/repositories/show.js  |  38 +++++
 app/controllers/repositories_controller.rb   |  19 +--
 app/views/repositories/index.html.erb        |  60 ++------
 app/views/repositories/show.html.erb         | 144 +++++++++++++++++++
 config/initializers/assets.rb                |   1 +
 config/locales/en.yml                        |   9 ++
 config/routes.rb                             |   2 -
 8 files changed, 213 insertions(+), 134 deletions(-)
 create mode 100644 app/assets/javascripts/repositories/show.js
 create mode 100644 app/views/repositories/show.html.erb

diff --git a/app/assets/javascripts/repositories/index.js b/app/assets/javascripts/repositories/index.js
index fed0920ed..f0fe68693 100644
--- a/app/assets/javascripts/repositories/index.js
+++ b/app/assets/javascripts/repositories/index.js
@@ -6,78 +6,8 @@
     animateSpinner();
     location.reload();
   }
-
-  function initImportRecordsModal() {
-    $('#importRecordsButton').off().on('click', function() {
-      $('#modal-import-records').modal('show');
-      _initParseRecordsModal();
-    });
-  }
-
-  function _initParseRecordsModal() {
-    $('#form-records-file').on('ajax:success', function(ev, data) {
-      $('#modal-import-records').modal('hide');
-      $(data.html).appendTo('body').promise().done(function() {
-        $('#parse-records-modal')
-          .modal('show')
-          .on('hidden.bs.modal', function() {
-            animateSpinner();
-            location.reload();
-          });
-        repositoryRecordsImporter();
-      });
-    }).on('ajax:error', function(ev, data) {
-      $(this).find('.form-group').addClass('has-error');
-      $(this).find('.form-group').find('.help-block').remove();
-      $(this).find('.form-group').append("<span class='help-block'>" +
-                                         data.responseJSON.message + '</span>');
-    });
-  }
-
-  function loadRepositoryTab() {
-    var param;
-    $('#repository-tabs a').on("click", function(e) {
-      e.preventDefault();
-      var pane = $(this);
-      $.ajax({
-        url: $(this).attr("data-url"),
-        type: "GET",
-        dataType: "json",
-        success: function (data) {
-        	var tabBody = $(pane.context.hash).find(".tab-content-body");
-          tabBody.html(data.html);
-          pane.tab('show').promise().done(function(el) {
-            initImportRecordsModal();
-            RepositoryDatatable.destroy()
-            RepositoryDatatable.init(el.attr('data-repo-table'));
-          });
-        },
-        error: function (error) {
-          // TODO
-        }
-      });
-    });
-
-    // on page load
-    if( param = getParam('repository') ){
-      // load selected tab
-      $('a[href="#custom_repo_'+param+'"]').click();
-    }
-    else {
-      // load first tab content
-      $('#repository-tabs a:first').click();
-    }
-
-    // clean tab content
-    $('a[data-toggle="tab"]').on('hide.bs.tab', function (e) {
-      $(".tab-content-body").html("");
-    })
-  }
-
-  $('.create-repository').initializeModal('#create-repo-modal');
-
+  
   $(document).ready(function() {
-    loadRepositoryTab();
-    initImportRecordsModal();
+    $('#create-new-repository').initializeModal('#create-repo-modal');
   });
 })(window);
diff --git a/app/assets/javascripts/repositories/show.js b/app/assets/javascripts/repositories/show.js
new file mode 100644
index 000000000..8bbda98e3
--- /dev/null
+++ b/app/assets/javascripts/repositories/show.js
@@ -0,0 +1,38 @@
+(function() {
+  'use strict';
+
+  function initImportRecordsModal() {
+    $('#importRecordsButton').off().on('click', function() {
+      $('#modal-import-records').modal('show');
+      _initParseRecordsModal();
+    });
+  }
+
+  function _initParseRecordsModal() {
+    $('#form-records-file').on('ajax:success', function(ev, data) {
+      $('#modal-import-records').modal('hide');
+      $(data.html).appendTo('body').promise().done(function() {
+        $('#parse-records-modal')
+          .modal('show')
+          .on('hidden.bs.modal', function() {
+            animateSpinner();
+            location.reload();
+          });
+        repositoryRecordsImporter();
+      });
+    }).on('ajax:error', function(ev, data) {
+      $(this).find('.form-group').addClass('has-error');
+      $(this).find('.form-group').find('.help-block').remove();
+      $(this).find('.form-group').append("<span class='help-block'>" +
+                                         data.responseJSON.message + '</span>');
+    });
+  }
+
+  function initialzerRepositoryTable() {
+    initImportRecordsModal();
+    RepositoryDatatable.destroy();
+    RepositoryDatatable.init('#' + $('.repository-table table').attr('id'));
+  }
+
+  $(document).ready(initialzerRepositoryTable);
+})()
diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index d1d30322b..03cdf18a8 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -12,20 +12,13 @@ class RepositoriesController < ApplicationController
     %i(create_new_modal create copy_modal copy)
 
   def index
-    render('repositories/index')
+    unless @repositories.length.zero? && current_team
+      redirect_to repository_path(@repositories.first) and return
+    end
+    render 'repositories/index'
   end
 
-  def show_tab
-    respond_to do |format|
-      format.json do
-        render json: {
-          html: render_to_string(
-            partial: 'repositories/repository.html.erb',
-            locals: { repository: @repository }
-          )
-        }
-      end
-    end
+  def show
   end
 
   def create_modal
@@ -287,7 +280,7 @@ class RepositoriesController < ApplicationController
   end
 
   def load_parent_vars
-    @team = Team.find_by_id(params[:team_id])
+    @team = current_team
     render_404 unless @team
     @repositories = @team.repositories.order(created_at: :asc)
   end
diff --git a/app/views/repositories/index.html.erb b/app/views/repositories/index.html.erb
index 2fcbbe935..1b98a2cd6 100644
--- a/app/views/repositories/index.html.erb
+++ b/app/views/repositories/index.html.erb
@@ -1,51 +1,19 @@
-<% provide(:head_title, t("repositories.index.head_title")) %>
+<% provide(:head_title, t("libraries.index.head_title")) %>
 
 <% if current_team %>
-  <%= render partial: "repositories/breadcrumbs.html.erb",
-             locals: { teams: @teams, current_team: current_team, type: @type } %>
-
-  <!-- Nav tabs -->
-  <ul class="nav nav-tabs nav-settings" role="tablist" id="repository-tabs">
-    <% @repositories.each do |repo| %>
-      <li role="presentation">
-        <a href="#custom_repo_<%= repo.id %>"
-           data-toggle="tab"
-           data-repo-table="#repository-table-<%= repo.id %>"
-           aria-controls="custom_repo_<%= repo.id %>"
-           data-url="<%=team_repository_show_tab_path(current_team, repo)%>"
-           title="<%=repo.name%>"><%= truncate(repo.name, length: Constants::NAME_TRUNCATION_LENGTH) %></a>
-      </li>
-    <% end %>
-
-    <!-- Add new repository tab -->
-    <li role="presentation"
-      <% unless can_create_repositories?(current_team) || current_team.repositories.count < Constants::REPOSITORIES_LIMIT %>
-        class="disabled"
-      <% end %>>
-      <a
-        <% if can_create_repositories?(current_team) && current_team.repositories.count < Constants::REPOSITORIES_LIMIT %>
-          href="<%= create_modal_team_repositories_path %>"
-          class='create-repository'
-          data-remote='true'
-        <% end %>>
-        <span class="glyphicon glyphicon-plus"></span>
-        <span class="hidden-xs">&nbsp;<%= t('repositories.index.add_new_repository_tab') %></span>
-      </a>
-    </li>
-  </ul>
-
-  <!-- Tab panes -->
-  <div class="tab-content">
-    <% @repositories.each do |repo| %>
-      <div class="tab-pane tab-pane-settings" id="custom_repo_<%= repo.id %>">
-        <!-- Tab Content -->
-        <div class="container-fluid">
-          <div class="tab-content-body"></div>
-        </div>
-      </div>
-    <% end %>
+  <%
+    # show only if no repositories present. If the team will have them we will
+    # handle this in left side navigation bar
+  %>
+  <div class="jumbotron text-center" style="margin-top:25%">
+    <strong><%=t 'libraries.index.no_libraries.text' %></strong>
+    <h2><strong><%=t 'libraries.index.no_libraries.title' %><strong></h2>
+    <br />
+    <a class="btn btn-info btn-lg"
+       id="create-new-repository"
+       href="<%= create_modal_team_repositories_path(current_team) %>"
+       data-remote="true"><%=t 'libraries.index.no_libraries.create_new_button' %></a>
   </div>
-
 <% else %>
   <!-- If member of no teams -->
   <div class="jumbotron">
@@ -54,6 +22,4 @@
   </div>
 <% end %>
 
-<%= stylesheet_link_tag 'datatables' %>
-<%= javascript_include_tag 'repositories/repository_datatable' %>
 <%= javascript_include_tag "repositories/index", "data-turbolinks-track" => true %>
diff --git a/app/views/repositories/show.html.erb b/app/views/repositories/show.html.erb
new file mode 100644
index 000000000..668ffdd51
--- /dev/null
+++ b/app/views/repositories/show.html.erb
@@ -0,0 +1,144 @@
+<% provide(:head_title, t("libraries.show.head_title", library: @repository.name)) %>
+
+<%= render partial: "repositories/delete_record_modal.html.erb" %>
+<%= render partial: "repositories/delete_column_modal.html.erb" %>
+<%= render partial: 'repositories/export_repository_modal.html.erb',
+           locals: { repository: @repository } %>
+
+<div id="alert-container"></div>
+
+<div id="repository-toolbar">
+
+  <% if can_create_repository_rows?(@repository.team) %>
+    <button type="button" class="btn btn-default editAdd" id="addRepositoryRecord" onclick="onClickAddRecord()">
+      <span class="glyphicon glyphicon-plus"></span>
+      <span class="hidden-xs"><%= t("repositories.add_new_record") %></span>
+    </button>
+    <button type="button" class="btn btn-default" id="importRecordsButton">
+      <span class="glyphicon glyphicon-cloud-upload"></span>
+      <span class="hidden-xs"><%= t('repositories.import_records.import') %></span>
+    </button>
+  <% end %>
+
+  <% if can_read_team?(@repository.team) %>
+    <a href="#" class="btn btn-default" id="exportRepositoriesButton" data-turbolinks="false">
+      <span class="glyphicon glyphicon-cloud-download"></span>
+      <span class="hidden-xs"><%= t("my_modules.repository.export") %></span>
+    </a>
+  <% end %>
+
+  <div class="repository-cog">
+    <div class="dropdown">
+      <div class="btn btn-default"
+           type="button"
+           data-toggle="dropdown"
+           aria-haspopup="true"
+           aria-expanded="true"
+           <%= "disabled" unless can_manage_repository?(@repository) || can_create_repositories?(@repository.team) %>>
+        <span class="glyphicon glyphicon-cog"></span>
+        <span class="caret"></span>
+      </div>
+      <% if can_manage_repository?(@repository) || can_create_repositories?(@repository.team) %>
+        <ul class="dropdown-menu pull-right">
+          <li class="dropdown-header">
+            <%= t("repositories.index.options_dropdown.header") %>
+          </li>
+          <% if can_manage_repository?(@repository) %>
+            <li>
+              <%= link_to t('repositories.index.options_dropdown.rename'),
+                          team_repository_rename_modal_path(current_team, repository_id: @repository),
+                          class: "rename-repo-option",
+                          remote: true %>
+            </li>
+          <% end %>
+          <% if can_create_repositories?(@repository.team) %>
+            <li>
+              <%= link_to t('repositories.index.options_dropdown.copy'),
+                          team_repository_copy_modal_path(current_team, repository_id: @repository),
+                          class: "copy-repo-option",
+                          remote: true %>
+            </li>
+          <% end %>
+          <% if can_manage_repository?(@repository) %>
+            <li role="separator" class="divider"></li>
+            <li>
+              <%= link_to t('repositories.index.modal_delete.delete'),
+                          team_repository_destroy_modal_path(current_team, repository_id: @repository),
+                          class: "delete-repo-option",
+                          remote: true %>
+            </li>
+          <% end %>
+        </ul>
+      <% end %>
+    </div>
+  </div>
+
+  <div id="datatables-buttons" style="display: inline;">
+    <div id="repository-columns-dropdown" class="dropdown">
+      <button class="btn btn-default dropdown-toggle" type="button" data-toggle="dropdown">
+        <%= t('repositories.columns') %>
+        <span class="caret"></span>
+      </button>
+      <ul class="dropdown-menu dropdown-menu-right smart-dropdown" id="repository-columns-list">
+        <% if can_create_repository_columns?(@repository.team) %>
+          <li class="add-new-column-form">
+            <div id="new-column-form" class="form-group" data-action="<%= repository_repository_columns_path(@repository) %>">
+              <div class="input-group">
+                <input class="form-control" id="new-column-name" placeholder="<%= t("repositories.column_new_text") %>">
+                <span class="input-group-btn">
+                  <a id="add-new-column-button" class="btn btn-primary">
+                    <%= t("repositories.column_create") %>
+                  </a>
+                </span>
+              </div>
+            </div>
+          </li>
+        <% end %>
+      </ul>
+    </div>
+  </div>
+</div>
+
+<div class="btn-group inline" id="saveCancel" data-toggle="buttons" style="display:none">
+  <button type="button" class="btn btn-primary" id="saveRecord" onclick="onClickSave()">
+    <span class="glyphicon glyphicon-save"></span>
+    <%= t("repositories.save_record") %>
+  </button>
+  <button type="button" class="btn btn-default" id="cancelSave" onclick="onClickCancel()">
+    <span class="glyphicon glyphicon-remove visible-xs-inline"></span>
+    <span class="hidden-xs"><%= t("repositories.cancel_save") %></span>
+  </button>
+</div>
+
+<!-- These buttons are appended to table in javascript, after table initialization -->
+<div class="toolbarButtons" style="display:none">
+  <button type="button" class="btn btn-default editAdd" id="editRepositoryRecord" onclick="onClickEdit()" disabled>
+    <span class="glyphicon glyphicon-pencil"></span>
+    <span class="hidden-xs-custom"><%= t("repositories.edit_record") %></span>
+  </button>
+
+  <% if can_manage_repository_rows?(@repository.team) %>
+    <button type="button" class="btn btn-default"
+      id="deleteRepositoryRecordsButton" data-target="#deleteRepositoryRecord" data-toggle="modal" disabled>
+      <span class="glyphicon glyphicon-trash"></span>
+      <span class="hidden-xs-custom"><%= t'repositories.delete_record' %></span>
+        <%= submit_tag I18n.t('repositories.delete_record'), :class => "hidden
+        delete_repository_records_submit" %>
+    </button>
+  <% end %>
+</div>
+
+<%= render partial: "repositories/repository_table.html.erb",
+           locals: {
+             repository: @repository,
+             repository_index_link: repository_table_index_path(@repository)
+           }
+%>
+<%= render partial: 'repositories/import_repository_records_modal.html.erb',
+                    locals: { repository: @repository } %>
+<%= javascript_include_tag 'repositories/edit', 'data-turbolinks-track' => true %>
+
+
+<%= stylesheet_link_tag 'datatables' %>
+<%= javascript_include_tag 'repositories/repository_datatable' %>
+<%= javascript_include_tag "repositories/show", "data-turbolinks-track" => true %>
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index a4d9c0cd0..38f4189e9 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -83,6 +83,7 @@ Rails.application.config.assets.precompile +=
 Rails.application.config.assets.precompile +=
   %w(repositories/my_module_repository.js)
 Rails.application.config.assets.precompile += %w(activities/index.js)
+Rails.application.config.assets.precompile += %w(repositories/show.js)
 
 # Libraries needed for Handsontable formulas
 Rails.application.config.assets.precompile += %w(lodash.js)
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 2c9316b69..adccc9d6a 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -984,6 +984,15 @@ en:
     no_records_unassigned_flash: "No items were unassigned from task"
     default_column: 'Name'
 
+  libraries:
+    index:
+      head_title: "Libraries"
+      no_libraries:
+        text: "You don't have any libraries."
+        title: "Please create your first Library"
+        create_new_button: "Create New Library"
+    show:
+      head_title: "Libraries | %{library}"
   repository_row:
     modal_info:
       head_title: "Information for record '%{repository_row}'"
diff --git a/config/routes.rb b/config/routes.rb
index 331b644cc..ba9becb4f 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -153,8 +153,6 @@ Rails.application.routes.draw do
           get 'create_modal', to: 'repositories#create_modal',
               defaults: { format: 'json' }
         end
-        get 'show_tab', to: 'repositories#show_tab',
-            defaults: { format: 'json' }
         get 'destroy_modal', to: 'repositories#destroy_modal',
             defaults: { format: 'json' }
         get 'rename_modal', to: 'repositories#rename_modal',

From 81df97f008b92237620e1ae4bba0ddfc348626a9 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 21 Mar 2018 09:22:55 +0100
Subject: [PATCH 02/23] add library sidebar and create new library button
 [fixes SCI-2121]

---
 .../stylesheets/themes/repositories.scss      |  8 ++++++
 app/assets/stylesheets/themes/scinote.scss    |  2 +-
 app/controllers/repositories_controller.rb    |  4 ++-
 app/views/repositories/_sidebar.html.erb      | 23 +++++++++++++++
 app/views/repositories/index.html.erb         | 10 ++++---
 app/views/repositories/show.html.erb          | 28 +++++++++++++------
 config/locales/en.yml                         |  2 ++
 7 files changed, 63 insertions(+), 14 deletions(-)
 create mode 100644 app/assets/stylesheets/themes/repositories.scss
 create mode 100644 app/views/repositories/_sidebar.html.erb

diff --git a/app/assets/stylesheets/themes/repositories.scss b/app/assets/stylesheets/themes/repositories.scss
new file mode 100644
index 000000000..a4244ac97
--- /dev/null
+++ b/app/assets/stylesheets/themes/repositories.scss
@@ -0,0 +1,8 @@
+#repository-columns-dropdown {
+  float: right;
+}
+
+.new-repository-button {
+  float: left;
+  margin-right: 5px;
+}
diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss
index 39ae3b334..6967c9b2a 100644
--- a/app/assets/stylesheets/themes/scinote.scss
+++ b/app/assets/stylesheets/themes/scinote.scss
@@ -2,7 +2,7 @@
 @import "mixins";
 @import "main_navigation";
 @import "buttons";
-
+@import "repositories";
 /** Layout **/
 
 body,
diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index 03cdf18a8..d0351a324 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -11,6 +11,8 @@ class RepositoriesController < ApplicationController
   before_action :check_create_permissions, only:
     %i(create_new_modal create copy_modal copy)
 
+  # layout 'fluid'
+
   def index
     unless @repositories.length.zero? && current_team
       redirect_to repository_path(@repositories.first) and return
@@ -46,7 +48,7 @@ class RepositoriesController < ApplicationController
         if @repository.save
           flash[:success] = t('repositories.index.modal_create.success_flash',
                               name: @repository.name)
-          render json: { url: team_repositories_path(repository: @repository) },
+          render json: { url: repository_path(@repository) },
             status: :ok
         else
           render json: @repository.errors,
diff --git a/app/views/repositories/_sidebar.html.erb b/app/views/repositories/_sidebar.html.erb
new file mode 100644
index 000000000..273fd0f17
--- /dev/null
+++ b/app/views/repositories/_sidebar.html.erb
@@ -0,0 +1,23 @@
+ <%= content_for :sidebar do %>
+  <div id="slide-panel" class="visible">
+    <div class="sidebar-header">
+      <div class="sidebar-header-title">
+        <h5><%=t "libraries.sidebar.title" %></h5>
+      </div>
+    </div>
+    <div class="sidebar-header-toggle">
+      <a href="" id="toggle-sidebar-link">
+        <span class="glyphicon glyphicon-play-circle"></span>
+      </a>
+    </div>
+    <div class="tree">
+      <ul>
+        <% repositories.each do |repository| %>
+          <% cache repository do %>
+            <li><%= link_to repository.name, repository_path(repository) %></li>
+          <% end %>
+        <% end %>
+      </ul>
+    </div>
+  </div>
+<% end %>
diff --git a/app/views/repositories/index.html.erb b/app/views/repositories/index.html.erb
index 1b98a2cd6..960f77ea1 100644
--- a/app/views/repositories/index.html.erb
+++ b/app/views/repositories/index.html.erb
@@ -1,6 +1,7 @@
 <% provide(:head_title, t("libraries.index.head_title")) %>
 
 <% if current_team %>
+  <%= render partial: "sidebar", locals: { repositories: @repositories } %>
   <%
     # show only if no repositories present. If the team will have them we will
     # handle this in left side navigation bar
@@ -9,10 +10,11 @@
     <strong><%=t 'libraries.index.no_libraries.text' %></strong>
     <h2><strong><%=t 'libraries.index.no_libraries.title' %><strong></h2>
     <br />
-    <a class="btn btn-info btn-lg"
-       id="create-new-repository"
-       href="<%= create_modal_team_repositories_path(current_team) %>"
-       data-remote="true"><%=t 'libraries.index.no_libraries.create_new_button' %></a>
+    <%= link_to t('libraries.index.no_libraries.create_new_button'),
+                create_modal_team_repositories_path(current_team),
+                class: "btn btn-info btn-lg",
+                id: "create-new-repository",
+                remote: true %>
   </div>
 <% else %>
   <!-- If member of no teams -->
diff --git a/app/views/repositories/show.html.erb b/app/views/repositories/show.html.erb
index 668ffdd51..6d1efcba6 100644
--- a/app/views/repositories/show.html.erb
+++ b/app/views/repositories/show.html.erb
@@ -1,10 +1,7 @@
 <% provide(:head_title, t("libraries.show.head_title", library: @repository.name)) %>
+<%= stylesheet_link_tag 'datatables' %>
 
-<%= render partial: "repositories/delete_record_modal.html.erb" %>
-<%= render partial: "repositories/delete_column_modal.html.erb" %>
-<%= render partial: 'repositories/export_repository_modal.html.erb',
-           locals: { repository: @repository } %>
-
+<%= render partial: "sidebar", locals: { repositories: @repositories } %>
 <div id="alert-container"></div>
 
 <div id="repository-toolbar">
@@ -73,7 +70,18 @@
     </div>
   </div>
 
+
   <div id="datatables-buttons" style="display: inline;">
+    <div class="new-repository-button">
+      <% if can_create_repositories?(@repository.team) %>
+        <%= link_to t('libraries.index.no_libraries.create_new_button'),
+                    create_modal_team_repositories_path(@repository.team),
+                    class: "btn btn-default",
+                    id: "create-new-repository",
+                    remote: true %>
+      <% end %>
+    </div>
+
     <div id="repository-columns-dropdown" class="dropdown">
       <button class="btn btn-default dropdown-toggle" type="button" data-toggle="dropdown">
         <%= t('repositories.columns') %>
@@ -136,9 +144,13 @@
 %>
 <%= render partial: 'repositories/import_repository_records_modal.html.erb',
                     locals: { repository: @repository } %>
+
+<%= render partial: "repositories/delete_record_modal.html.erb" %>
+<%= render partial: "repositories/delete_column_modal.html.erb" %>
+<%= render partial: 'repositories/export_repository_modal.html.erb',
+           locals: { repository: @repository } %>
+
 <%= javascript_include_tag 'repositories/edit', 'data-turbolinks-track' => true %>
-
-
-<%= stylesheet_link_tag 'datatables' %>
 <%= javascript_include_tag 'repositories/repository_datatable' %>
 <%= javascript_include_tag "repositories/show", "data-turbolinks-track" => true %>
+<%= javascript_include_tag "repositories/index", "data-turbolinks-track" => true %>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 2ae86722d..2549c012b 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -986,6 +986,8 @@ en:
     default_column: 'Name'
 
   libraries:
+    sidebar:
+      title: "Libraries"
     index:
       head_title: "Libraries"
       no_libraries:

From e42fc3117b6d3a18df3b7c87e6f6e6273275a24c Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Mon, 26 Mar 2018 13:19:09 +0200
Subject: [PATCH 03/23] Implement search in file repository cells and improve
 performance [SCI-2111]

---
 Gemfile.lock                                  |  5 +-
 app/controllers/search_controller.rb          | 98 ++++++++++++-------
 app/models/asset.rb                           | 51 +++-------
 app/views/search/index.html.erb               | 42 +++++---
 app/views/search/results/_assets.html.erb     | 25 +++--
 .../results/partials/_asset_text.html.erb     | 32 +++++-
 .../partials/_repository_row_text.html.erb    |  7 ++
 .../partials/_repository_text.html.erb        |  7 ++
 config/initializers/extends.rb                |  6 +-
 config/locales/en.yml                         |  3 +-
 10 files changed, 174 insertions(+), 102 deletions(-)
 create mode 100644 app/views/search/results/partials/_repository_row_text.html.erb
 create mode 100644 app/views/search/results/partials/_repository_text.html.erb

diff --git a/Gemfile.lock b/Gemfile.lock
index ecfaef70f..339037097 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,10 +1,11 @@
 GIT
   remote: https://github.com/biosistemika/canaid
-  revision: f2000c19b75e66ea929a44cb0575262b7f5fc13e
+  revision: 943ae9b9801819fd2513f6ab9e1143ad8de523ce
   branch: master
   specs:
-    canaid (1.0.1)
+    canaid (1.0.2)
       devise (>= 3.4.1)
+      docile (>= 1.1.0)
       rails (>= 4)
 
 GIT
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 19f912ba4..f3b87e4e0 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -4,6 +4,8 @@ class SearchController < ApplicationController
   def index
     redirect_to new_search_path unless @search_query
 
+    @search_id = params[:search_id] ? params[:search_id] : generate_search_id
+
     count_search_results
 
     search_projects if @search_category == :projects
@@ -86,6 +88,10 @@ class SearchController < ApplicationController
 
   protected
 
+  def generate_search_id
+    SecureRandom.urlsafe_base64(32)
+  end
+
   def search_by_name(model)
     model.search(current_user,
                  true,
@@ -109,52 +115,61 @@ class SearchController < ApplicationController
   end
 
   def count_by_repository
-    count_total = 0
-    search_results = Repository.search(current_user,
-                                       @search_query,
-                                       Constants::SEARCH_NO_LIMIT,
-                                       nil,
-                                       match_case: @search_case,
-                                       whole_word: @search_whole_word,
-                                       whole_phrase: @search_whole_phrase)
-    @repository_search_count = {}
-    current_user.teams.includes(:repositories).each do |team|
-      team_results = {}
-      team_results[:count] = 0
-      team_results[:repositories] = {}
-      team.repositories.each do |repository|
-        repository_results = {}
-        repository_results[:id] = repository.id
-        repository_results[:count] = 0
-        search_results.each do |result|
-          if repository.id == result.id
-            count_total += result.counter
-            repository_results[:count] += result.counter
+    @repository_search_count =
+      Rails.cache.fetch("#{@search_id}/repository_search_count",
+                        expires_in: 5.minutes) do
+        search_count = {}
+        search_results = Repository.search(current_user,
+                                           @search_query,
+                                           Constants::SEARCH_NO_LIMIT,
+                                           nil,
+                                           match_case: @search_case,
+                                           whole_word: @search_whole_word,
+                                           whole_phrase: @search_whole_phrase)
+
+        current_user.teams.includes(:repositories).each do |team|
+          team_results = {}
+          team_results[:count] = 0
+          team_results[:repositories] = {}
+          team.repositories.each do |repository|
+            repository_results = {}
+            repository_results[:id] = repository.id
+            repository_results[:count] = 0
+            search_results.each do |result|
+              if repository.id == result.id
+                repository_results[:count] += result.counter
+              end
+            end
+            team_results[:repositories][repository.name] = repository_results
+            team_results[:count] += repository_results[:count]
           end
+          search_count[team.name] = team_results
         end
-        team_results[:repositories][repository.name] = repository_results
-        team_results[:count] += repository_results[:count]
+        search_count
       end
-      @repository_search_count[team.name] = team_results
+
+    count_total = 0
+    @repository_search_count.each_value do |team_results|
+      count_total += team_results[:count]
     end
     count_total
   end
 
   def count_search_results
-    @project_search_count = count_by_name Project
-    @experiment_search_count = count_by_name Experiment
-    @module_search_count = count_by_name MyModule
-    @result_search_count = count_by_name Result
-    @tag_search_count = count_by_name Tag
-    @report_search_count = count_by_name Report
-    @protocol_search_count = count_by_name Protocol
-    @step_search_count = count_by_name Step
-    @checklist_search_count = count_by_name Checklist
-    @sample_search_count = count_by_name Sample
+    @project_search_count = fetch_cached_count Project
+    @experiment_search_count = fetch_cached_count Experiment
+    @module_search_count = fetch_cached_count MyModule
+    @result_search_count = fetch_cached_count Result
+    @tag_search_count = fetch_cached_count Tag
+    @report_search_count = fetch_cached_count Report
+    @protocol_search_count = fetch_cached_count Protocol
+    @step_search_count = fetch_cached_count Step
+    @checklist_search_count = fetch_cached_count Checklist
+    @sample_search_count = fetch_cached_count Sample
     @repository_search_count_total = count_by_repository
-    @asset_search_count = count_by_name Asset
-    @table_search_count = count_by_name Table
-    @comment_search_count = count_by_name Comment
+    @asset_search_count = fetch_cached_count Asset
+    @table_search_count = fetch_cached_count Table
+    @comment_search_count = fetch_cached_count Comment
 
     @search_results_count = @project_search_count
     @search_results_count += @experiment_search_count
@@ -172,6 +187,15 @@ class SearchController < ApplicationController
     @search_results_count += @comment_search_count
   end
 
+  def fetch_cached_count(type)
+    exp = 5.minutes
+    Rails.cache.fetch(
+      "#{@search_id}/#{type.name.underscore}_search_count", expires_in: exp
+    ) do
+      count_by_name type
+    end
+  end
+
   def search_projects
     @project_results = []
     @project_results = search_by_name(Project) if @project_search_count > 0
diff --git a/app/models/asset.rb b/app/models/asset.rb
index 318cc104a..055db8873 100644
--- a/app/models/asset.rb
+++ b/app/models/asset.rb
@@ -91,37 +91,19 @@ class Asset < ApplicationRecord
 
   def self.search(
     user,
-    include_archived,
+    _include_archived,
     query = nil,
     page = 1,
     _current_team = nil,
     options = {}
   )
-    step_ids =
-      Step
-      .search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT)
-      .joins(:step_assets)
-      .distinct
-      .pluck('step_assets.id')
 
-    result_ids =
-      Result
-      .search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT)
-      .joins(:result_asset)
-      .distinct
-      .pluck('result_assets.id')
-
-    ids =
+    new_query =
       Asset
-      .select(:id)
       .distinct
-      .joins('LEFT OUTER JOIN step_assets ON step_assets.asset_id = assets.id')
-      .joins('LEFT OUTER JOIN result_assets ON ' \
-             'result_assets.asset_id = assets.id')
-      .joins('LEFT JOIN asset_text_data ON ' \
-             'assets.id = asset_text_data.asset_id')
-      .where('(step_assets.id IN (?) OR result_assets.id IN (?))',
-             step_ids, result_ids)
+      .select('assets.*')
+      .left_outer_joins(:asset_text_datum)
+      .where(team: user.teams)
 
     a_query = s_query = ''
 
@@ -144,7 +126,7 @@ class Asset < ApplicationRecord
       a_query = '\\y(' + a_query + ')\\y'
       s_query = s_query.tr('\'', '"')
 
-      ids = ids.where(
+      new_query = new_query.where(
         "(trim_html_tags(assets.file_file_name) #{like} ? " \
         "OR asset_text_data.data_vector @@ to_tsquery(?))",
         a_query,
@@ -165,7 +147,7 @@ class Asset < ApplicationRecord
                      .map { |t| t + ':*' }
                      .join('|')
                      .tr('\'', '"')
-      ids = ids.where(
+      new_query = new_query.where(
         "(trim_html_tags(assets.file_file_name) #{like} ANY (array[?]) " \
         "OR asset_text_data.data_vector @@ to_tsquery(?))",
         a_query,
@@ -175,19 +157,14 @@ class Asset < ApplicationRecord
 
     # Show all results if needed
     if page != Constants::SEARCH_NO_LIMIT
-      ids = ids
-            .limit(Constants::SEARCH_LIMIT)
-            .offset((page - 1) * Constants::SEARCH_LIMIT)
+      new_query.select("ts_headline(data, to_tsquery('" +
+                       sanitize_sql_for_conditions(s_query) +
+                       "'), 'StartSel=<mark>, StopSel=</mark>') headline")
+               .limit(Constants::SEARCH_LIMIT)
+               .offset((page - 1) * Constants::SEARCH_LIMIT)
+    else
+      new_query
     end
-
-    Asset
-      .joins('LEFT JOIN asset_text_data ON ' \
-             ' assets.id = asset_text_data.asset_id')
-      .select('assets.*')
-      .select("ts_headline(data, to_tsquery('" +
-              sanitize_sql_for_conditions(s_query) +
-              "'), 'StartSel=<mark>, StopSel=</mark>') headline")
-      .where('assets.id IN (?)', ids)
   end
 
   def is_image?
diff --git a/app/views/search/index.html.erb b/app/views/search/index.html.erb
index b00a61fcb..b42d20441 100644
--- a/app/views/search/index.html.erb
+++ b/app/views/search/index.html.erb
@@ -51,7 +51,8 @@
         >
           <a href="?<%= {category: 'projects', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @project_search_count %></span>
             <span class="glyphicon glyphicon-blackboard"></span>
             <%= t'Projects' %>
@@ -64,7 +65,8 @@
         >
           <a href="?<%= {category: 'experiments', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @experiment_search_count %></span>
             <%= fa_icon 'flask' %>
             <%= t'Experiments' %>
@@ -77,7 +79,8 @@
         >
           <a href="?<%= {category: 'modules', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @module_search_count %></span>
             <span class="glyphicon glyphicon-credit-card"></span>
             <%= t'Modules' %>
@@ -90,7 +93,8 @@
         >
           <a href="?<%= {category: 'results', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @result_search_count %></span>
             <span class="glyphicon glyphicon-modal-window"></span>
             <%= t'Results' %>
@@ -103,7 +107,8 @@
         >
           <a href="?<%= {category: 'tags', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @tag_search_count %></span>
             <span class="glyphicon glyphicon-tags"></span>
             <%= t'Tags' %>
@@ -116,7 +121,8 @@
         >
           <a href="?<%= {category: 'reports', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @report_search_count %></span>
             <span class="glyphicon glyphicon-align-left"></span>
             <%= t'Reports' %>
@@ -129,7 +135,8 @@
         >
           <a href="?<%= {category: 'protocols', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @protocol_search_count %></span>
             <span class="glyphicon glyphicon-list-alt"></span>
             <%= t'Protocols' %>
@@ -142,7 +149,8 @@
         >
           <a href="?<%= {category: 'steps', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @step_search_count %></span>
             <span class="glyphicon glyphicon-circle-arrow-right"></span>
             <%= t'Steps' %>
@@ -155,7 +163,8 @@
         >
           <a href="?<%= {category: 'checklists', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @checklist_search_count %></span>
             <span class="glyphicon glyphicon-list"></span>
             <%= t'Checklists' %>
@@ -168,7 +177,8 @@
         >
           <a href="?<%= {category: 'samples', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @sample_search_count %></span>
             <span class="glyphicon glyphicon-tint"></span>
             <%= t'Samples' %>
@@ -182,7 +192,8 @@
         >
           <a href="?<%= {category: 'assets', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @asset_search_count %></span>
             <span class="glyphicon glyphicon-file"></span>
             <%= t'Assets' %>
@@ -195,7 +206,8 @@
         >
           <a href="?<%= {category: 'tables', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @table_search_count %></span>
             <span class="glyphicon glyphicon-th"></span>
             <%= t'Tables' %>
@@ -208,7 +220,8 @@
         >
           <a href="?<%= {category: 'comments', q: @search_query,
                          whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                         match_case: @search_case, utf8: '✓'}.to_query %>">
+                         match_case: @search_case, utf8: '✓',
+                         search_id: @search_id}.to_query %>">
             <span class="badge pull-right"><%= @comment_search_count %></span>
             <span class="glyphicon glyphicon-comment"></span>
             <%= t'Comments' %>
@@ -229,7 +242,8 @@
               <a href="?<%= {category: 'repositories',
                              repository: values[:id], q: @search_query,
                              whole_word: @search_whole_word, whole_phrase: @search_whole_phrase,
-                             match_case: @search_case, utf8: '✓'}.to_query %>">
+                             match_case: @search_case, utf8: '✓',
+                             search_id: @search_id}.to_query %>">
                 <span class="badge pull-right"><%= values[:count] %></span>
                 <%= repository %>
               </a>
diff --git a/app/views/search/results/_assets.html.erb b/app/views/search/results/_assets.html.erb
index f33c3b0fe..255a8b769 100644
--- a/app/views/search/results/_assets.html.erb
+++ b/app/views/search/results/_assets.html.erb
@@ -12,13 +12,6 @@
     <%= render partial: "search/results/partials/asset_text.html.erb", locals: { asset: asset, query: search_query } %>
   </h5>
 
-  <!-- Display asset contents if it exists -->
-  <% if asset.headline.present? && !asset.headline.empty? && asset.headline.include?("<mark>") %>
-    <blockquote class="blockquote-search">
-      <p><%= highlight(sanitize_input(asset.headline), search_query.strip.split(/\s+/)) %></p>
-    </blockquote>
-  <% end %>
-
   <p>
     <span>
       <%=t "search.index.created_at" %>
@@ -93,6 +86,24 @@
         <%= render partial: "search/results/partials/team_text.html.erb",
                    locals: { team: asset.result.my_module.experiment.project.team } %>
       </span>
+    <% elsif asset.repository_asset_value %>
+      <span>
+        <%=t "search.index.repository_row" %>
+        <%= render partial: "search/results/partials/repository_row_text.html.erb",
+                   locals: { repository_row: asset.repository_asset_value.repository_cell.repository_row } %>
+      </span>
+      <br>
+      <span>
+        <%=t "search.index.repository" %>
+        <%= render partial: "search/results/partials/repository_text.html.erb",
+                   locals: { repository: asset.repository_asset_value.repository_cell.repository_row.repository } %>
+      </span>
+      <br>
+      <span>
+        <%=t "search.index.team" %>
+        <%= render partial: "search/results/partials/team_text.html.erb",
+                   locals: { team: asset.team } %>
+      </span>
     <% end %>
   </p>
 
diff --git a/app/views/search/results/partials/_asset_text.html.erb b/app/views/search/results/partials/_asset_text.html.erb
index 1e81800a3..f5a483393 100644
--- a/app/views/search/results/partials/_asset_text.html.erb
+++ b/app/views/search/results/partials/_asset_text.html.erb
@@ -1,15 +1,43 @@
 <% query ||= nil %>
+<% asset_read_allowed = false %>
 <% text = query.present? ? highlight(asset.file_file_name, query.strip.split(/\s+/)) : asset.file_file_name %>
 
 <% if asset.step %>
   <% protocol = asset.step.protocol %>
   <% if can_read_protocol_in_module?(protocol) ||
-        can_read_protocol_in_repository?(protocol) ||
-        (asset.result && can_read_experiment?(protocol.my_module.experiment)) %>
+        can_read_protocol_in_repository?(protocol) %>
+    <% asset_read_allowed = true %>
     <a href="<%= download_asset_path asset %>" target="_blank">
       <%= text %>
     </a>
+  <% else %>
+    <%= text %>
+  <% end %>
+<% elsif asset.result %>
+  <% if can_read_experiment?(asset.result.my_module.experiment) %>
+    <% asset_read_allowed = true %>
+    <a href="<%= download_asset_path asset %>" target="_blank">
+      <%= text %>
+    </a>
+  <% else %>
+    <%= text %>
+  <% end %>
+<% elsif asset.repository_asset_value %>
+  <% if can_read_team?(asset.repository_asset_value.repository_cell.repository_row.repository.team) %>
+    <% asset_read_allowed = true %>
+    <a href="<%= download_asset_path asset %>" target="_blank">
+      <%= text %>
+    </a>
+  <% else %>
+    <%= text %>
   <% end %>
 <% else %>
   <%= text %>
 <% end %>
+
+<!-- Display asset contents if it exists -->
+<% if asset_read_allowed && asset.headline.present? && asset.headline.include?("<mark>") %>
+  <blockquote class="blockquote-search">
+    <p><%= highlight(sanitize_input(asset.headline), query.strip.split(/\s+/)) %></p>
+  </blockquote>
+<% end %>
diff --git a/app/views/search/results/partials/_repository_row_text.html.erb b/app/views/search/results/partials/_repository_row_text.html.erb
new file mode 100644
index 000000000..ea6c23340
--- /dev/null
+++ b/app/views/search/results/partials/_repository_row_text.html.erb
@@ -0,0 +1,7 @@
+<% if can_read_team?(repository_row.repository.team) %>
+  <%= route_to_other_team repository_path(id: repository_row.repository.id),
+                          repository_row.repository.team,
+                          repository_row.name %>
+<% else %>
+  <%= repository_row.name %>
+<% end %>
diff --git a/app/views/search/results/partials/_repository_text.html.erb b/app/views/search/results/partials/_repository_text.html.erb
new file mode 100644
index 000000000..fbc7f2d5d
--- /dev/null
+++ b/app/views/search/results/partials/_repository_text.html.erb
@@ -0,0 +1,7 @@
+<% if can_read_team?(repository.team) %>
+  <%= route_to_other_team repository_path(id: repository.id),
+                          repository.team,
+                          repository.name %>
+<% else %>
+  <%= repository.name %>
+<% end %>
diff --git a/config/initializers/extends.rb b/config/initializers/extends.rb
index bd0a90886..a70e4b38c 100644
--- a/config/initializers/extends.rb
+++ b/config/initializers/extends.rb
@@ -52,11 +52,13 @@ class Extends
   # Extra attributes used for search in repositories, text columns
   # are only supported
   REPOSITORY_EXTRA_SEARCH_ATTR = ['repository_text_values.data',
-                                  'repository_list_items.data']
+                                  'repository_list_items.data',
+                                  'assets.file_file_name']
 
   # Array of includes used in search query for repository rows
   REPOSITORY_SEARCH_INCLUDES = [:repository_text_value,
-                                repository_list_value: :repository_list_item]
+                                repository_list_value: :repository_list_item,
+                                repository_asset_value: :asset]
 
   # List of implemented core API versions
   API_VERSIONS = ['20170715']
diff --git a/config/locales/en.yml b/config/locales/en.yml
index b675d7f22..3e30a9f39 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -152,6 +152,8 @@ en:
       description: "Description: "
       no_description: "No description"
       team: "Team: "
+      repository: "Repository: "
+      repository_row: "Repository item: "
       project: "Project: "
       experiment: "Experiment: "
       protocol: "Protocol: "
@@ -211,7 +213,6 @@ en:
         one: "1 day"
         other: "%{count} days"
       module_one_day_due_html: "Task <em>%{module}</em> is due in less than 1 day."
-      new_comment: "New comment"
       user_role: "Role: "
       user_full_name: "User: "
       edit_user: "Edit role"

From fac5875cfd2827483376c7e28e6914bc4b108fe4 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Mon, 26 Mar 2018 16:18:09 +0200
Subject: [PATCH 04/23] Add repository name to record info modal [SCI-2205]

---
 app/assets/stylesheets/repositories.scss                   | 7 +++++++
 app/views/repositories/_repository_row_info_modal.html.erb | 4 ++++
 config/locales/en.yml                                      | 1 +
 3 files changed, 12 insertions(+)

diff --git a/app/assets/stylesheets/repositories.scss b/app/assets/stylesheets/repositories.scss
index 01190665d..fefa88357 100644
--- a/app/assets/stylesheets/repositories.scss
+++ b/app/assets/stylesheets/repositories.scss
@@ -1,3 +1,5 @@
+@import "constants";
+
 .repositories-dropdown-menu {
   height: auto;
   max-height: 400px;
@@ -24,3 +26,8 @@
   float: right;
   text-align: inherit;
 }
+
+.breadcrumb.breadcrumb-repository {
+  background-color: $color-concrete;
+  margin-bottom: 15px;
+}
diff --git a/app/views/repositories/_repository_row_info_modal.html.erb b/app/views/repositories/_repository_row_info_modal.html.erb
index f73a40feb..b107e9786 100644
--- a/app/views/repositories/_repository_row_info_modal.html.erb
+++ b/app/views/repositories/_repository_row_info_modal.html.erb
@@ -7,6 +7,10 @@
       </div>
 
       <div class="modal-body">
+        <ol class="breadcrumb breadcrumb-repository">
+          <span class="fa fa-cubes" aria-hidden="true"></span>
+          <%= "#{t('repositories.repository')}: #{@repository_row.repository.name}" %>
+        </ol>
         <p>
           <span>
             <%= t "repository_row.modal_info.added_on" %>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index f15a06373..3f61578f2 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -873,6 +873,7 @@ en:
       success_flash: "Table result successfully deleted."
 
   repositories:
+    repository: "Repository"
     index:
       head_title: "Repositories"
       title: "Repositories"

From 22afa61b11784a538f6c744cc26596cc8a90153d Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Wed, 28 Mar 2018 13:54:01 +0200
Subject: [PATCH 05/23] refactor colors

---
 app/assets/stylesheets/application.scss       |   2 +
 app/assets/stylesheets/constants.scss         | 500 ++++++++++++++++--
 app/assets/stylesheets/extend/bootstrap.scss  |   2 +-
 app/assets/stylesheets/my_modules.scss        |   6 +-
 app/assets/stylesheets/notifications.scss     |  20 +-
 app/assets/stylesheets/partials/_sidebar.scss |  12 +-
 .../stylesheets/partials/_tree_view.scss      |   6 +-
 app/assets/stylesheets/projects.scss          |  48 +-
 app/assets/stylesheets/reports.scss           |  36 +-
 .../stylesheets/sample_types_groups.scss      |   2 +-
 .../stylesheets/themes/main_navigation.scss   |  52 +-
 app/assets/stylesheets/themes/menu_bar.scss   |   4 +-
 app/assets/stylesheets/themes/scinote.scss    |  87 +--
 app/javascript/src/styles/constants.scss      |  30 +-
 app/javascript/src/styles/main.scss           |  26 +-
 config/initializers/constants.rb              |  25 +-
 16 files changed, 624 insertions(+), 234 deletions(-)

diff --git a/app/assets/stylesheets/application.scss b/app/assets/stylesheets/application.scss
index eeb5db641..dcd1af2ad 100644
--- a/app/assets/stylesheets/application.scss
+++ b/app/assets/stylesheets/application.scss
@@ -9,6 +9,8 @@
  *= require introjs
  *= stub reports_pdf
  */
+
+@import "constants";
 @import "bootstrap-sprockets";
 @import "bootstrap";
 @import "bootstrap-datetimepicker";
diff --git a/app/assets/stylesheets/constants.scss b/app/assets/stylesheets/constants.scss
index 771cc6433..8e0c00d85 100644
--- a/app/assets/stylesheets/constants.scss
+++ b/app/assets/stylesheets/constants.scss
@@ -2,53 +2,32 @@
 // Colors
 //==============================================================================
 
-// Theme colors
-$color-theme-primary: #41B0E0;
-$color-theme-secondary: #8fd13f;
-$color-theme-dark: #6d6e71;
-
 // Grayscale colors
-$color-border: #DDDDDD;
-$color-list-separator: #BDC3C7;
 $color-white: #fff;
 $color-alabaster: #fcfcfc;
-$color-snow: #f9f9f9;
-$color-wild-sand: #f5f5f5;
 $color-concrete: #f2f2f2;
-$color-gallery: #eee;
 $color-gainsboro: #e3e3e3;
 $color-alto: #d2d2d2;
 $color-silver: #c5c5c5;
-$color-dark-gray: #adadad;
 $color-silver-chalice: #a0a0a0;
-$color-gray: #909088;
 $color-dove-gray: #666;
 $color-emperor: #555;
-$color-mine-shaft: #333;
-$color-nero: #262626;
 $color-black: #000;
-$color-cloud: rgba(0, 0, 0, .1);
-$color-gray-light-yadcf: #ccc;
-$color-gray-dark-yadcf: #a9a9a9;
 
-// Miscelaneous colors
-$color-mystic: #eaeff2;
-$color-candlelight: #ffda23;
-$color-orange: #ff900b;
-$color-saturated-green: #008600;
-$color-confirmation-green: #25AE88;
-$color-blue-yadcf: #337ab7;
+// Theme colors
+$brand-default: $color-white;
+$brand-primary: #41b0e0;
+$brand-success: #5cb85c;
+$brand-info: #5bc0de;
+$brand-warning: #f0ad4e;
+$brand-danger: #d9534f;
+$brand-other: #9b59b6;
+$brand-extra: #34495e;
+$brand-primary-light: #dcedf6;
+$brand-success-light: #e2eed8;
+$brand-warning-light: #fcf7e4;
+$brand-danger-light: #efdfdf;
 
-// Red colors
-$color-mojo: #cf4b48;
-$color-apple-blossom: #a94442;
-$color-milano-red: #a70b05;
-
-// Colors for specific intents
-$color-visited-link: #23527c;
-
-// Overlay shade for drag'n dropdown
-$color-drag-overlay: rgba(0, 0, 0, .4);
 
 //==============================================================================
 // Other
@@ -56,3 +35,456 @@ $color-drag-overlay: rgba(0, 0, 0, .4);
 
 // Some big value which is still supported by all browsers
 $infinity: 9999999;
+
+
+//==============================================================================
+// Bootstrap
+//==============================================================================
+
+// Grayscale Colors in bootstrap
+$gray-darker: $color-black;
+$gray-dark: $color-emperor;
+$gray: $color-emperor;
+$gray-light: $color-dove-gray;
+$gray-lighter: $color-concrete;
+
+// // Scaffolding
+// $body-bg: #fff;
+// $text-color: #ee3df0;
+// $link-color: $brand-primary;
+// $link-hover-color: darken($link-color, 15%);
+// $link-hover-decoration: underline;
+
+// // Typography
+// $font-family-sans-serif: "Open Sans", Arial, Helvetica, sans-serif;
+// $font-family-serif: Georgia, "Times New Roman", Times, serif;
+// $font-family-monospace: Menlo, Monaco, Consolas, "Courier New", monospace;
+// $font-family-base: $font-family-sans-serif;
+// $font-size-base: 14px;
+// $font-size-large: ceil(($font-size-base * 1.25));
+// $font-size-small: ceil(($font-size-base * 0.85));
+// $font-size-h1: floor(($font-size-base * 2.6));
+// $font-size-h2: floor(($font-size-base * 2.15));
+// $font-size-h3: ceil(($font-size-base * 1.7));
+// $font-size-h4: ceil(($font-size-base * 1.25));
+// $font-size-h5: $font-size-base;
+// $font-size-h6: ceil(($font-size-base * 0.85));
+// $line-height-base: 1.428571429;
+// $line-height-computed: floor(($font-size-base * $line-height-base));
+// $headings-font-family: inherit;
+// $headings-font-weight: 500;
+// $headings-line-height: 1.1;
+// $headings-color: inherit;
+//
+// // Iconography
+// $icon-font-path: "../fonts/";
+// $icon-font-name: "glyphicons-halflings-regular";
+// $icon-font-svg-id: "glyphicons_halflingsregular";
+//
+// // Components
+// $padding-base-vertical: 6px;
+// $padding-base-horizontal: 12px;
+// $padding-large-vertical: 10px;
+// $padding-large-horizontal: 16px;
+// $padding-small-vertical: 5px;
+// $padding-small-horizontal: 10px;
+// $padding-xs-vertical: 1px;
+// $padding-xs-horizontal: 5px;
+// $line-height-large: 1.3333333;
+// $line-height-small: 1.5;
+// $border-radius-base: 4px;
+// $border-radius-large: 6px;
+// $border-radius-small: 3px;
+// $component-active-color: #fff;
+// $component-active-bg: $brand-primary;
+// $caret-width-base: 4px;
+// $caret-width-large: 5px;
+//
+// // Tables
+// $table-cell-padding: 8px;
+// $table-condensed-cell-padding: 5px;
+// $table-bg: transparent;
+// $table-bg-accent: #f9f9f9;
+// $table-bg-hover: #f5f5f5;
+// $table-bg-active: $table-bg-hover;
+// $table-border-color: #ddd;
+//
+// // Buttons
+// $btn-font-weight: normal;
+// $btn-default-color: #333;
+// $btn-default-bg: $brand-default;
+// $btn-default-border: #ccc;
+// $btn-primary-color: #fff;
+// $btn-primary-bg: $brand-primary;
+// $btn-primary-border: darken($btn-primary-bg, 5%);
+// $btn-success-color: #fff;
+// $btn-success-bg: $brand-success;
+// $btn-success-border: darken($btn-success-bg, 5%);
+// $btn-info-color: #fff;
+// $btn-info-bg: $brand-info;
+// $btn-info-border: darken($btn-info-bg, 5%);
+// $btn-warning-color: #fff;
+// $btn-warning-bg: $brand-warning;
+// $btn-warning-border: darken($btn-warning-bg, 5%);
+// $btn-danger-color: #fff;
+// $btn-danger-bg: $brand-danger;
+// $btn-danger-border: darken($btn-danger-bg, 5%);
+// $btn-link-disabled-color: $gray-light;
+// $btn-border-radius-base: $border-radius-base;
+// $btn-border-radius-large: $border-radius-large;
+// $btn-border-radius-small: $border-radius-small;
+//
+// // Forms
+// $input-bg: #fff;
+// $input-bg-disabled: $gray-lighter;
+// $input-color: $gray;
+// $input-border: #ccc;
+// $input-border-radius: $border-radius-base;
+// $input-border-radius-large: $border-radius-large;
+// $input-border-radius-small: $border-radius-small;
+// $input-border-focus: #66afe9;
+// $input-color-placeholder: #999;
+// $input-height-base: ($line-height-computed + ($padding-base-vertical * 2) + 2);
+// $input-height-large: (ceil($font-size-large * $line-height-large) + ($padding-large-vertical * 2) + 2);
+// $input-height-small: (floor($font-size-small * $line-height-small) + ($padding-small-vertical * 2) + 2);
+// $form-group-margin-bottom: 15px;
+// $legend-color: $gray-dark;
+// $legend-border-color: #e5e5e5;
+// $input-group-addon-bg: $gray-lighter;
+// $input-group-addon-border-color: $input-border;
+// $cursor-disabled: not-allowed;
+//
+// // Dropdowns
+// $dropdown-bg: #fff;
+// $dropdown-border: rgba(0,0,0,.15);
+// $dropdown-fallback-border: #ccc;
+// $dropdown-divider-bg: #e5e5e5;
+// $dropdown-link-color: $gray-dark;
+// $dropdown-link-hover-color: darken($gray-dark, 5%);
+// $dropdown-link-hover-bg: #f5f5f5;
+// $dropdown-link-active-color: $component-active-color;
+// $dropdown-link-active-bg: $component-active-bg;
+// $dropdown-link-disabled-color: $gray-light;
+// $dropdown-header-color: $gray-light;
+// $dropdown-caret-color: #000;
+//
+// // Media queries breakpoints
+// $screen-xs: 480px;
+// $screen-xs-min: $screen-xs;
+// $screen-phone: $screen-xs-min;
+// $screen-sm: 768px;
+// $screen-sm-min: $screen-sm;
+// $screen-tablet: $screen-sm-min;
+// $screen-md: 992px;
+// $screen-md-min: $screen-md;
+// $screen-desktop: $screen-md-min;
+// $screen-lg: 1200px;
+// $screen-lg-min: $screen-lg;
+// $screen-lg-desktop: $screen-lg-min;
+// $screen-xs-max: ($screen-sm-min - 1);
+// $screen-sm-max: ($screen-md-min - 1);
+// $screen-md-max: ($screen-lg-min - 1);
+//
+// // Grid system
+// $grid-columns: 12;
+// $grid-gutter-width: 30px;
+// $grid-float-breakpoint: $screen-sm-min;
+// $grid-float-breakpoint-max: ($grid-float-breakpoint - 1);
+//
+// // Container sizes
+// $container-tablet: (720px + $grid-gutter-width);
+// $container-sm: $container-tablet;
+// $container-desktop: (940px + $grid-gutter-width);
+// $container-md: $container-desktop;
+// $container-large-desktop: (1140px + $grid-gutter-width);
+// $container-lg: $container-large-desktop;
+//
+// // Navbar
+// $navbar-height: 50px;
+// $navbar-margin-bottom: $line-height-computed;
+// $navbar-border-radius: $border-radius-base;
+// $navbar-padding-horizontal: floor(($grid-gutter-width / 2));
+// $navbar-padding-vertical: (($navbar-height - $line-height-computed) / 2);
+// $navbar-collapse-max-height: 340px;
+// $navbar-default-color: #777;
+// $navbar-default-bg: #f8f8f8;
+// $navbar-default-border: darken($navbar-default-bg, 6.5%);
+// $navbar-default-link-color: #777;
+// $navbar-default-link-hover-color: #333;
+// $navbar-default-link-hover-bg: transparent;
+// $navbar-default-link-active-color: #555;
+// $navbar-default-link-active-bg: darken($navbar-default-bg, 6.5%);
+// $navbar-default-link-disabled-color: #ccc;
+// $navbar-default-link-disabled-bg: transparent;
+// $navbar-default-brand-color: $navbar-default-link-color;
+// $navbar-default-brand-hover-color: darken($navbar-default-brand-color, 10%);
+// $navbar-default-brand-hover-bg: transparent;
+// $navbar-default-toggle-hover-bg: #ddd;
+// $navbar-default-toggle-icon-bar-bg: #888;
+// $navbar-default-toggle-border-color: #ddd;
+//
+// // Inverted navbar
+// $navbar-inverse-color: lighten($gray-light, 15%);
+// $navbar-inverse-bg: #222;
+// $navbar-inverse-border: darken($navbar-inverse-bg, 10%);
+// $navbar-inverse-link-color: lighten($gray-light, 15%);
+// $navbar-inverse-link-hover-color: #fff;
+// $navbar-inverse-link-hover-bg: transparent;
+// $navbar-inverse-link-active-color: $navbar-inverse-link-hover-color;
+// $navbar-inverse-link-active-bg: darken($navbar-inverse-bg, 10%);
+// $navbar-inverse-link-disabled-color: #444;
+// $navbar-inverse-link-disabled-bg: transparent;
+// $navbar-inverse-brand-color: $navbar-inverse-link-color;
+// $navbar-inverse-brand-hover-color: #fff;
+// $navbar-inverse-brand-hover-bg: transparent;
+// $navbar-inverse-toggle-hover-bg: #333;
+// $navbar-inverse-toggle-icon-bar-bg: #fff;
+// $navbar-inverse-toggle-border-color: #333;
+//
+// // Navs
+// $nav-link-padding: 10px 15px;
+// $nav-link-hover-bg: $gray-lighter;
+// $nav-disabled-link-color: $gray-light;
+// $nav-disabled-link-hover-color: $gray-light;
+//
+// // Tabs
+// $nav-tabs-border-color: #ddd;
+// $nav-tabs-link-hover-border-color: $gray-lighter;
+// $nav-tabs-active-link-hover-bg: $body-bg;
+// $nav-tabs-active-link-hover-color: $gray;
+// $nav-tabs-active-link-hover-border-color: #ddd;
+// $nav-tabs-justified-link-border-color: #ddd;
+// $nav-tabs-justified-active-link-border-color: $body-bg;
+//
+// // Pills
+// $nav-pills-border-radius: $border-radius-base;
+// $nav-pills-active-link-hover-bg: $component-active-bg;
+// $nav-pills-active-link-hover-color: $component-active-color;
+//
+// // Pagination
+// $pagination-color: $link-color;
+// $pagination-bg: #fff;
+// $pagination-border: #ddd;
+// $pagination-hover-color: $link-hover-color;
+// $pagination-hover-bg: $gray-lighter;
+// $pagination-hover-border: #ddd;
+// $pagination-active-color: #fff;
+// $pagination-active-bg: $brand-primary;
+// $pagination-active-border: $brand-primary;
+// $pagination-disabled-color: $gray-light;
+// $pagination-disabled-bg: #fff;
+// $pagination-disabled-border: #ddd;
+//
+// // Pager
+// $pager-bg: $pagination-bg;
+// $pager-border: $pagination-border;
+// $pager-border-radius: 15px;
+// $pager-hover-bg: $pagination-hover-bg;
+// $pager-active-bg: $pagination-active-bg;
+// $pager-active-color: $pagination-active-color;
+// $pager-disabled-color: $pagination-disabled-color;
+//
+// // Jumbotron
+// $jumbotron-padding: 30px;
+// $jumbotron-color: inherit;
+// $jumbotron-bg: $gray-lighter;
+// $jumbotron-heading-color: inherit;
+// $jumbotron-font-size: ceil(($font-size-base * 1.5));
+// $jumbotron-heading-font-size: ceil(($font-size-base * 4.5));
+//
+// // Form states and alerts
+// $state-success-text: #3c763d;
+// $state-success-bg: #dff0d8;
+// $state-success-border: adjust-hue(darken($state-success-bg, 5%), -10);
+// $state-info-text: #31708f;
+// $state-info-bg: #d9edf7;
+// $state-info-border: adjust-hue(darken($state-info-bg, 7%), -10);
+// $state-warning-text: #8a6d3b;
+// $state-warning-bg: #fcf8e3;
+// $state-warning-border: adjust-hue(darken($state-warning-bg, 5%), -10);
+// $state-danger-text: #a94442;
+// $state-danger-bg: #f2dede;
+// $state-danger-border: adjust-hue(darken($state-danger-bg, 5%), -10);
+//
+// // Tooltips
+// $tooltip-max-width: 200px;
+// $tooltip-color: #fff;
+// $tooltip-bg: #000;
+// $tooltip-opacity: .9;
+// $tooltip-arrow-width: 5px;
+// $tooltip-arrow-color: $tooltip-bg;
+//
+// // Popovers
+// $popover-bg: #fff;
+// $popover-max-width: 276px;
+// $popover-border-color: rgba(0,0,0,.2);
+// $popover-fallback-border-color: #ccc;
+// $popover-title-bg: darken($popover-bg, 3%);
+// $popover-arrow-width: 10px;
+// $popover-arrow-color: $popover-bg;
+// $popover-arrow-outer-width: ($popover-arrow-width + 1);
+// $popover-arrow-outer-color: fadein($popover-border-color, 5%);
+// $popover-arrow-outer-fallback-color: darken($popover-fallback-border-color, 20%);
+//
+// // Labels
+// $label-default-bg: $gray-light;
+// $label-primary-bg: $brand-primary;
+// $label-success-bg: $brand-success;
+// $label-info-bg: $brand-info;
+// $label-warning-bg: $brand-warning;
+// $label-danger-bg: $brand-danger;
+// $label-color: #fff;
+// $label-link-hover-color: #fff;
+//
+// // Modals
+// $modal-inner-padding: 15px;
+// $modal-title-padding: 15px;
+// $modal-title-line-height: $line-height-base;
+// $modal-content-bg: #fff;
+// $modal-content-border-color: rgba(0,0,0,.2);
+// $modal-content-fallback-border-color: #999;
+// $modal-backdrop-bg: #000;
+// $modal-backdrop-opacity: .5;
+// $modal-header-border-color: #e5e5e5;
+// $modal-footer-border-color: $modal-header-border-color;
+// $modal-lg: 900px;
+// $modal-md: 600px;
+// $modal-sm: 300px;
+//
+// // Alerts
+// $alert-padding: 15px;
+// $alert-border-radius: $border-radius-base;
+// $alert-link-font-weight: bold;
+// $alert-success-bg: $state-success-bg;
+// $alert-success-text: $state-success-text;
+// $alert-success-border: $state-success-border;
+// $alert-info-bg: $state-info-bg;
+// $alert-info-text: $state-info-text;
+// $alert-info-border: $state-info-border;
+// $alert-warning-bg: $state-warning-bg;
+// $alert-warning-text: $state-warning-text;
+// $alert-warning-border: $state-warning-border;
+// $alert-danger-bg: $state-danger-bg;
+// $alert-danger-text: $state-danger-text;
+// $alert-danger-border: $state-danger-border;
+//
+// // Progress bars
+// $progress-bg: #f5f5f5;
+// $progress-bar-color: #fff;
+// $progress-border-radius: $border-radius-base;
+// $progress-bar-bg: $brand-primary;
+// $progress-bar-success-bg: $brand-success;
+// $progress-bar-warning-bg: $brand-warning;
+// $progress-bar-danger-bg: $brand-danger;
+// $progress-bar-info-bg: $brand-info;
+//
+// // List group
+// $list-group-bg: #fff;
+// $list-group-border: #ddd;
+// $list-group-border-radius: $border-radius-base;
+// $list-group-hover-bg: #f5f5f5;
+// $list-group-active-color: $component-active-color;
+// $list-group-active-bg: $component-active-bg;
+// $list-group-active-border: $list-group-active-bg;
+// $list-group-active-text-color: lighten($list-group-active-bg, 40%);
+// $list-group-disabled-color: $gray-light;
+// $list-group-disabled-bg: $gray-lighter;
+// $list-group-disabled-text-color: $list-group-disabled-color;
+// $list-group-link-color: #555;
+// $list-group-link-hover-color: $list-group-link-color;
+// $list-group-link-heading-color: #333;
+//
+// // Panels
+// $panel-bg: #fff;
+// $panel-body-padding: 15px;
+// $panel-heading-padding: 10px 15px;
+// $panel-footer-padding: $panel-heading-padding;
+// $panel-border-radius: $border-radius-base;
+// $panel-inner-border: #ddd;
+// $panel-footer-bg: #f5f5f5;
+// $panel-default-text: $gray-dark;
+// $panel-default-border: #ddd;
+// $panel-default-heading-bg: #f5f5f5;
+// $panel-primary-text: #fff;
+// $panel-primary-border: $brand-primary;
+// $panel-primary-heading-bg: $brand-primary;
+// $panel-success-text: $state-success-text;
+// $panel-success-border: $state-success-border;
+// $panel-success-heading-bg: $state-success-bg;
+// $panel-info-text: $state-info-text;
+// $panel-info-border: $state-info-border;
+// $panel-info-heading-bg: $state-info-bg;
+// $panel-warning-text: $state-warning-text;
+// $panel-warning-border: $state-warning-border;
+// $panel-warning-heading-bg: $state-warning-bg;
+// $panel-danger-text: $state-danger-text;
+// $panel-danger-border: $state-danger-border;
+// $panel-danger-heading-bg: $state-danger-bg;
+//
+// // Thumbnails
+// $thumbnail-padding: 4px;
+// $thumbnail-bg: $body-bg;
+// $thumbnail-border: #ddd;
+// $thumbnail-border-radius: $border-radius-base;
+// $thumbnail-caption-color: $text-color;
+// $thumbnail-caption-padding: 9px;
+//
+// // Wells
+// $well-bg: #f5f5f5;
+// $well-border: darken($well-bg, 7%);
+//
+// // Badges
+// $badge-color: #fff;
+// $badge-link-hover-color: #fff;
+// $badge-bg: $gray-light;
+// $badge-active-color: $link-color;
+// $badge-active-bg: #fff;
+// $badge-font-weight: bold;
+// $badge-line-height: 1;
+// $badge-border-radius: 10px;
+//
+// // Breadcrumbs
+// $breadcrumb-padding-vertical: 8px;
+// $breadcrumb-padding-horizontal: 15px;
+// $breadcrumb-bg: #f5f5f5;
+// $breadcrumb-color: #ccc;
+// $breadcrumb-active-color: $gray-light;
+// $breadcrumb-separator: "/";
+//
+// // Carousel
+// $carousel-text-shadow: 0 1px 2px rgba(0,0,0,.6);
+// $carousel-control-color: #fff;
+// $carousel-control-width: 15%;
+// $carousel-control-opacity: .5;
+// $carousel-control-font-size: 20px;
+// $carousel-indicator-active-bg: #fff;
+// $carousel-indicator-border-color: #fff;
+// $carousel-caption-color: #fff;
+//
+// // Close
+// $close-font-weight: bold;
+// $close-color: #000;
+// $close-text-shadow: 0 1px 0 #fff;
+//
+// // Code
+// $code-color: #c7254e;
+// $code-bg: #f9f2f4;
+// $kbd-color: #fff;
+// $kbd-bg: #333;
+// $pre-bg: #f5f5f5;
+// $pre-color: $gray-dark;
+// $pre-border-color: #ccc;
+// $pre-scrollable-max-height: 340px;
+//
+// // Type
+// $component-offset-horizontal: 180px;
+// $text-muted: $gray-light;
+// $abbr-border-color: $gray-light;
+// $headings-small-color: $gray-light;
+// $blockquote-small-color: $gray-light;
+// $blockquote-font-size: ($font-size-base * 1.25);
+// $blockquote-border-color: $gray-lighter;
+// $page-header-border-color: $gray-lighter;
+// $dl-horizontal-offset: $component-offset-horizontal;
+// $dl-horizontal-breakpoint: $grid-float-breakpoint;
+// $hr-border: $gray-lighter;
diff --git a/app/assets/stylesheets/extend/bootstrap.scss b/app/assets/stylesheets/extend/bootstrap.scss
index ac2030716..830422c4d 100644
--- a/app/assets/stylesheets/extend/bootstrap.scss
+++ b/app/assets/stylesheets/extend/bootstrap.scss
@@ -14,7 +14,7 @@
 
 // Active tab with error should retain error color if clicked on again
 .nav-tabs > li.active.has-error > a {
-  color: $color-apple-blossom;
+  color: $brand-danger;
 }
 
 @media (max-width: 886px) {
diff --git a/app/assets/stylesheets/my_modules.scss b/app/assets/stylesheets/my_modules.scss
index 896653b10..c1d22bed7 100644
--- a/app/assets/stylesheets/my_modules.scss
+++ b/app/assets/stylesheets/my_modules.scss
@@ -8,15 +8,15 @@
 .task-due-date,
 .task-state-label {
   .alert-green {
-    color: $color-saturated-green;
+    color: $brand-success;
   }
 
   .alert-yellow {
-    color: $color-candlelight;
+    color: $brand-warning;
   }
 
   .alert-red {
-    color: $color-milano-red;
+    color: $brand-danger;
   }
 }
 
diff --git a/app/assets/stylesheets/notifications.scss b/app/assets/stylesheets/notifications.scss
index 4cfa15824..9ef0f991b 100644
--- a/app/assets/stylesheets/notifications.scss
+++ b/app/assets/stylesheets/notifications.scss
@@ -31,7 +31,7 @@
     padding-top: 10px;
 
     &:hover {
-      background-color: $color-mystic;
+      background-color: $brand-primary-light;
     }
 
     &.no-notifications {
@@ -40,7 +40,7 @@
   }
 
   .unseen {
-    border-left: 4px solid $color-theme-primary;
+    border-left: 4px solid $brand-primary;
   }
 
   .text-center {
@@ -49,9 +49,9 @@
   }
 
   .assignment {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: inline-block;
     font-size: 13px;
     height: 30px;
@@ -60,9 +60,9 @@
   }
 
   .system-message {
-    background-color: $color-theme-secondary;
+    background-color: $brand-default;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: inline-block;
     font-size: 13px;
     height: 30px;
@@ -71,9 +71,9 @@
   }
 
   .deliver {
-    background-color: $color-orange;
+    background-color: $brand-warning;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: inline-block;
     font-size: 13px;
     height: 30px;
@@ -85,7 +85,7 @@
 
 .notifications-footer {
 
-  background-color: $color-mystic;
+  background-color: $brand-primary-light;
 
   .btn-more-notifications {
     border-bottom: 1px solid $color-alto;
@@ -96,7 +96,7 @@
     text-align: center;
 
     &:hover {
-      background-color: $color-mystic;
+      background-color: $brand-primary-light;
     }
   }
 }
diff --git a/app/assets/stylesheets/partials/_sidebar.scss b/app/assets/stylesheets/partials/_sidebar.scss
index 8fb20bf6a..1ecba2cb7 100644
--- a/app/assets/stylesheets/partials/_sidebar.scss
+++ b/app/assets/stylesheets/partials/_sidebar.scss
@@ -38,8 +38,8 @@ $toggle-btn-size: 50px;
 
       .sidebar-header {
         height: $toggle-btn-size;
-        background: $color-theme-primary;
-        border-bottom: 2px solid darken($color-theme-primary, 10%);
+        background: $brand-primary;
+        border-bottom: 2px solid darken($brand-primary, 10%);
 
         .sidebar-header-title {
           width: inherit;
@@ -64,9 +64,9 @@ $toggle-btn-size: 50px;
         margin-left: ($wrapper-width - $toggle-btn-size);
         margin-top: -$toggle-btn-size;
         font-size: 20pt;
-        background: $color-theme-primary;
-        border-left: 2px solid darken($color-theme-primary, 10%);
-        border-bottom: 2px solid darken($color-theme-primary, 10%);
+        background: $brand-primary;
+        border-left: 2px solid darken($brand-primary, 10%);
+        border-bottom: 2px solid darken($brand-primary, 10%);
 
         // Animations
         @include transition(margin-left 0.5s ease);
@@ -118,7 +118,7 @@ $toggle-btn-size: 50px;
         @include transition(margin-left 0.5s ease);
 
         span {
-          color: darken($color-theme-primary, 10%);
+          color: darken($brand-primary, 10%);
 
           @include rotate-animation(0.5s, 0deg);
           @include transition(color 0.5s ease);
diff --git a/app/assets/stylesheets/partials/_tree_view.scss b/app/assets/stylesheets/partials/_tree_view.scss
index 440c188c9..a48fc1adb 100644
--- a/app/assets/stylesheets/partials/_tree_view.scss
+++ b/app/assets/stylesheets/partials/_tree_view.scss
@@ -18,7 +18,7 @@
   }
 
   .first-indent {
-    background-color: $color-wild-sand;
+    background-color: $color-concrete;
     padding-left: 30px;
   }
 
@@ -49,7 +49,7 @@
     }
 
     &.active > span {
-      background-color: $color-theme-primary;
+      background-color: $brand-primary;
       color: $color-white;
       font-weight: bold;
 
@@ -74,7 +74,7 @@
       color: $color-emperor;
 
       &:hover {
-        color: $color-theme-primary;
+        color: $brand-primary;
       }
     }
 
diff --git a/app/assets/stylesheets/projects.scss b/app/assets/stylesheets/projects.scss
index fa92a85e4..7477d6001 100644
--- a/app/assets/stylesheets/projects.scss
+++ b/app/assets/stylesheets/projects.scss
@@ -2,8 +2,8 @@
 @import "mixins";
 
 // Some color definitions
-$color-group-hover: $color-theme-primary;
-$color-module-hover: $color-theme-secondary;
+$color-group-hover: $brand-primary;
+$color-module-hover: $brand-default;
 
 /* Canvas index page */
 
@@ -112,7 +112,7 @@ $color-module-hover: $color-theme-secondary;
     cursor: pointer;
 
     &:hover {
-      color: $color-theme-primary;
+      color: $brand-primary;
       padding: 2px 9px 4px 9px;
     }
   }
@@ -122,7 +122,7 @@ $color-module-hover: $color-theme-secondary;
   border: 2px solid green;
 }
 .jsplumb-drag .title {
-  background-color: $color-theme-primary !important;
+  background-color: $brand-primary !important;
   color: $color-white !important;
 }
 path, ._jsPlumb_endpoint {
@@ -132,7 +132,7 @@ path, ._jsPlumb_endpoint {
   fill: $color-white;
 }
 .ep-hover svg * {
-  fill: $color-theme-primary;
+  fill: $brand-primary;
 }
 
 /* EDIT MODE MODULE */
@@ -140,16 +140,16 @@ path, ._jsPlumb_endpoint {
   opacity: 0.7;
 }
 .module.dragged > .panel-heading {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
   color: $color-white;
 }
 .module.collided {
   .overlay {
     display: block;
     z-index: 21;
-    background-color: $color-milano-red;
-    border: 1px solid $color-milano-red;
-    @include box-shadow(0 0 0 1pt $color-milano-red);
+    background-color: $brand-danger;
+    border: 1px solid $brand-danger;
+    @include box-shadow(0 0 0 1pt $brand-danger);
     border-radius: 4px;
     position: absolute;
     top: 0;
@@ -223,28 +223,28 @@ path, ._jsPlumb_endpoint {
   }
 
   &.alert-green .panel-body {
-    color: $color-saturated-green;
+    color: $brand-success;
     font-weight: bold;
 
     .due-date-link {
-      color: $color-saturated-green;
+      color: $brand-success;
     }
   }
 
   &.alert-yellow .panel-body {
-    color: $color-candlelight;
+    color: $brand-warning;
     font-weight: bold;
 
     .due-date-link {
-      color: $color-candlelight;
+      color: $brand-warning;
     }
   }
   &.alert-red .panel-body {
-    color: $color-milano-red;
+    color: $brand-danger;
     font-weight: bold;
 
     .due-date-link {
-      color: $color-milano-red;
+      color: $brand-danger;
     }
   }
 }
@@ -265,18 +265,18 @@ path, ._jsPlumb_endpoint {
   }
 
   &.alert-green {
-    border-color: $color-saturated-green;
+    border-color: $brand-success;
     border-radius: 8px;
     border-width: 4px;
   }
 
   &.alert-yellow {
-    border-color: $color-candlelight;
+    border-color: $brand-warning;
     border-width: 4px;
     border-radius: 8px;
   }
   &.alert-red {
-    border-color: $color-milano-red;
+    border-color: $brand-danger;
     border-width: 4px;
     border-radius: 8px;
   }
@@ -332,7 +332,7 @@ path, ._jsPlumb_endpoint {
     margin-top: 20%;
 
     a {
-      color: $color-mine-shaft;
+      color: $color-emperor;
     }
   }
 
@@ -344,14 +344,14 @@ path, ._jsPlumb_endpoint {
   }
 
   &.alert-green {
-    border-color: $color-saturated-green;
+    border-color: $brand-success;
   }
 
   &.alert-yellow {
-    border-color: $color-candlelight;
+    border-color: $brand-warning;
   }
   &.alert-red {
-  border-color: $color-milano-red;
+  border-color: $brand-danger;
   }
 }
 
@@ -362,7 +362,7 @@ li.group-hover {
 }
 li.module-hover {
   a {
-    color: $color-theme-primary;
+    color: $brand-primary;
     text-decoration: underline;
   }
 }
@@ -508,7 +508,7 @@ li.module-hover {
 }
 
 .big-plus {
-  color: $color-mystic;
+  color: $brand-primary-light;
   display: block;
   font-size: 250px;
   margin: 20px 0;
diff --git a/app/assets/stylesheets/reports.scss b/app/assets/stylesheets/reports.scss
index 33647fdbf..4027665be 100644
--- a/app/assets/stylesheets/reports.scss
+++ b/app/assets/stylesheets/reports.scss
@@ -148,7 +148,7 @@ label {
     opacity: 0.7;
     padding: 15px;
     border-radius: 5px;
-    border: 4px $color-theme-primary solid;
+    border: 4px $brand-primary solid;
 
     .plus-icon {
       bottom: 16px !important;
@@ -166,7 +166,7 @@ label {
       .filler {
         display: block;
         height: 4px;
-        background-color: $color-theme-primary;
+        background-color: $brand-primary;
         border-radius: 1px;
         margin-top: 8px;
         margin-bottom: 8px;
@@ -183,7 +183,7 @@ label {
   }
 
   .plus-icon {
-    color: $color-theme-primary;
+    color: $brand-primary;
     display: block;
     text-align: center;
     width: 40px;
@@ -201,7 +201,7 @@ label {
   opacity: 1.0;
 
   .filler {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
 
     .plus-icon span {
       font-weight: bold;
@@ -240,8 +240,8 @@ label {
   }
 
   &:hover {
-    background-color: $color-mystic;
-    @include box-shadow(0 0 2px 15px $color-mystic);
+    background-color: $brand-primary-light;
+    @include box-shadow(0 0 2px 15px $brand-primary-light);
 
     & > .report-element-header {
 
@@ -266,7 +266,7 @@ label {
   }
 
   &:hover > .report-element-body .project-name {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 }
 
@@ -297,7 +297,7 @@ label {
   }
 
   &:hover > .report-element-body .module-name {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 }
 
@@ -329,7 +329,7 @@ label {
   }
 
   &:hover > .report-element-header {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 
   .report-element-body {
@@ -368,7 +368,7 @@ label {
 /** Step element style  */
 .report-step-element {
   &:hover > .report-element-body .step-name {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 }
 
@@ -388,7 +388,7 @@ label {
 
   &:hover > .report-element-header {
     .attachment-icon {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 }
@@ -403,7 +403,7 @@ label {
 
   &:hover > .report-element-header {
     .table-name {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 }
@@ -417,7 +417,7 @@ label {
   }
 
   &:hover > .report-element-header .file-name {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 }
 
@@ -438,7 +438,7 @@ label {
   }
 
   &:hover > .report-element-header .checklist-name {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 }
 
@@ -475,7 +475,7 @@ label {
 
   &:hover > .report-element-header {
     .comments-icon,.comments-name {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 }
@@ -504,7 +504,7 @@ label {
 
   &:hover > .report-element-header {
     .samples-icon,.samples-name {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 }
@@ -524,7 +524,7 @@ label {
   &:hover > .report-element-header {
     .repository-icon,
     .repository-name {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 }
@@ -559,7 +559,7 @@ label {
 
   &:hover > .report-element-header {
     .activity-icon,.activity-name {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 }
diff --git a/app/assets/stylesheets/sample_types_groups.scss b/app/assets/stylesheets/sample_types_groups.scss
index c6b41fc7c..6abf8e741 100644
--- a/app/assets/stylesheets/sample_types_groups.scss
+++ b/app/assets/stylesheets/sample_types_groups.scss
@@ -45,7 +45,7 @@
   }
 
   .glyphicon-ok {
-    color: $color-theme-secondary;
+    color: $brand-default;
   }
 
   .glyphicon {
diff --git a/app/assets/stylesheets/themes/main_navigation.scss b/app/assets/stylesheets/themes/main_navigation.scss
index 94c0d7d98..903bf6744 100644
--- a/app/assets/stylesheets/themes/main_navigation.scss
+++ b/app/assets/stylesheets/themes/main_navigation.scss
@@ -12,9 +12,9 @@
   }
 
   #count-notifications {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
     border-radius: 5px;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: none;
     font-size: 11px;
     font-weight: bold;
@@ -69,7 +69,7 @@
   }
 
   .unseen {
-    border-left: 4px solid $color-theme-primary;
+    border-left: 4px solid $brand-primary;
   }
 
   .text-center {
@@ -84,9 +84,9 @@
   }
 
   .assignment {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: block;
     font-size: 23px;
     height: 45px;
@@ -95,9 +95,9 @@
   }
 
   .deliver {
-    background-color: $color-orange;
+    background-color: $brand-warning;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: block;
     font-size: 23px;
     height: 45px;
@@ -106,9 +106,9 @@
   }
 
   .system-message {
-    background-color: $color-theme-secondary;
+    background-color: $brand-default;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: block;
     font-size: 23px;
     height: 45px;
@@ -117,8 +117,8 @@
   }
 
   .notifications-dropdown-header {
-    background-color: $color-theme-primary;
-    color: $color-wild-sand;
+    background-color: $brand-primary;
+    color: $color-concrete;
     font-weight: bold;
     padding: 8px;
 
@@ -128,7 +128,7 @@
   }
 
   .notifications-dropdown-footer {
-    background-color: $color-mystic;
+    background-color: $brand-primary-light;
     padding: 8px;
     text-align: center;
   }
@@ -158,10 +158,10 @@
 }
 
 #search-bar {
-  border-color: $color-border;
+  border-color: $color-alto;
   .btn-default {
-    background-color: $color-theme-primary;
-    border-color: $color-theme-primary;
+    background-color: $brand-primary;
+    border-color: $brand-primary;
     color: $color-white;
   }
 
@@ -188,7 +188,7 @@
     padding: 10px 15px;
 
     &.active {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
   }
 
@@ -233,9 +233,9 @@
   }
 
   .assignment {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: block !important;
     font-size: 15px;
     height: 30px;
@@ -247,9 +247,9 @@
   }
 
   .system-message {
-    background-color: $color-theme-secondary;
+    background-color: $brand-default;
     border-radius: 50%;
-    color: $color-wild-sand;
+    color: $color-concrete;
     display: block !important;
     font-size: 15px;
     height: 30px;
@@ -274,13 +274,13 @@
   }
 
   .glyphicon-ok-sign {
-    color: $color-confirmation-green;
+    color: $brand-success;
     margin-left: -10px;
     margin-right: 10px;
   }
 
   .team-name-item {
-    border-bottom: 1px solid $color-list-separator;
+    border-bottom: 1px solid $color-silver-chalice;
     padding-bottom: 8px;
     padding-top: 5px;
   }
@@ -293,13 +293,13 @@
   }
 
   .btn-group {
-    border-color: $color-border;
+    border-color: $color-alto;
     margin-top: 8px;
   }
 
   .btn-primary {
-    background-color: $color-theme-primary;
-    border-color: $color-theme-primary;
+    background-color: $brand-primary;
+    border-color: $brand-primary;
   }
 
   .dropdown-menu {
@@ -340,7 +340,7 @@
 }
 
 .custom-nav-dropdown {
-  border: 1px solid $color-border;
+  border: 1px solid $color-alto;
   padding: 10px 0 10px 30px;
 }
 
diff --git a/app/assets/stylesheets/themes/menu_bar.scss b/app/assets/stylesheets/themes/menu_bar.scss
index 781043b8e..7e2a9d012 100644
--- a/app/assets/stylesheets/themes/menu_bar.scss
+++ b/app/assets/stylesheets/themes/menu_bar.scss
@@ -16,7 +16,7 @@
     padding-right: 4px;
 
     & > a {
-      color: $color-gray;
+      color: $color-silver-chalice;
       display: grid;
       font-size: 12px;
       margin-left: auto;
@@ -33,7 +33,7 @@
       background-color: $color-gainsboro;
       margin-right: 4px;
       padding-right: 0;
-      @include box-shadow(4px 0 0 $color-theme-primary);
+      @include box-shadow(4px 0 0 $brand-primary);
 
       & > a {
         color: $color-emperor;
diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss
index 39ae3b334..07004b8e2 100644
--- a/app/assets/stylesheets/themes/scinote.scss
+++ b/app/assets/stylesheets/themes/scinote.scss
@@ -101,7 +101,7 @@ body {
 }
 
 a {
-  color: $color-theme-primary;
+  color: $brand-primary;
 }
 
 .jumbotron {
@@ -109,7 +109,7 @@ a {
 }
 
 .badge {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
   font-size: 11px;
   border-radius: 5px;
 }
@@ -128,7 +128,7 @@ a {
 }
 
 .bg-primary {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
 }
 
 /* this rule is strict because the order of css files is not correct */
@@ -137,7 +137,7 @@ a {
 }
 
 mark,.mark {
-  background-color: $color-candlelight;
+  background-color: $brand-warning;
 }
 
 .label-default {
@@ -145,12 +145,12 @@ mark,.mark {
 }
 
 .label-primary {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
 }
 
 .circle {
   @extend .badge;
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
   border-radius: 1em;
 
   &.disabled {
@@ -173,10 +173,10 @@ a[data-toggle="tooltip"] {
 
   & > li.has-error {
     & > a {
-      color: $color-apple-blossom;
+      color: $brand-danger;
 
       &:hover {
-        color: $color-mojo;
+        color: $brand-danger;
       }
     }
   }
@@ -185,7 +185,7 @@ a[data-toggle="tooltip"] {
 .has-error {
   .ql-container.ql-snow,
   .ql-toolbar.ql-snow {
-    border: 1px solid $color-apple-blossom;
+    border: 1px solid $brand-danger;
   }
 }
 
@@ -196,7 +196,7 @@ a[data-toggle="tooltip"] {
 .nav-pills {
   & > li {
     a {
-      color: $color-theme-primary;
+      color: $brand-primary;
     }
 
     &:not(.active):hover a {
@@ -205,7 +205,7 @@ a[data-toggle="tooltip"] {
 
     &.active a {
       color: $color-white;
-      background-color: $color-theme-primary;
+      background-color: $brand-primary;
     }
   }
 }
@@ -220,7 +220,7 @@ a[data-toggle="tooltip"] {
 
 .nav-tabs-less > li.active > a {
   &,&:hover,&:focus {
-    color: $color-theme-secondary;
+    color: $brand-default;
     background-color: transparent;
     border-color: transparent;
   }
@@ -228,7 +228,7 @@ a[data-toggle="tooltip"] {
 
 .tag.label.label-info {
   font-size: 100%;
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
 }
 
 #secondary-navigation {
@@ -273,14 +273,14 @@ a[data-toggle="tooltip"] {
       text-transform: uppercase;
 
       & > a {
-        color: $color-gray;
+        color: $color-silver-chalice;
 
         span {
           //width: 14px;
         }
       }
       &.active {
-        @include box-shadow(0 4px 0 $color-theme-primary);
+        @include box-shadow(0 4px 0 $brand-primary);
 
         &> a {
           font-weight: bold;
@@ -538,16 +538,16 @@ ul.double-line > li {
 .pagination > .active > span,
 .pagination > .active > span:hover,
 .pagination > .active > span:focus {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
 }
 
 .pagination > li > a,
 .pagination > li > span {
-  color: $color-theme-primary;
+  color: $brand-primary;
 }
 
 .panel-default > .panel-heading {
-  background-color: $color-mystic;
+  background-color: $brand-primary-light;
 
   &>.panel-title {
     overflow: hidden;
@@ -558,15 +558,15 @@ ul.double-line > li {
 
 .panel-project {
   .panel-heading {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
     color: $color-white;
   }
 }
 
 .panel-archive {
   .panel-heading {
-    background-color: darken($color-mystic, 5%);
-    color: lighten($color-mine-shaft, 15%);
+    background-color: darken($brand-primary-light, 5%);
+    color: lighten($color-emperor, 15%);
   }
 }
 
@@ -637,11 +637,11 @@ ul.double-line > li {
 
     li.notification.alert-red > .date-time {
       font-weight: bold;
-      color: $color-milano-red;
+      color: $brand-danger;
     }
     li.notification.alert-yellow > .date-time {
       font-weight: bold;
-      color: $color-candlelight;
+      color: $brand-warning;
     }
   }
 }
@@ -653,7 +653,7 @@ ul.double-line > li {
   margin-bottom: 0;
 
   &> .panel-heading {
-    background-color: $color-mystic;
+    background-color: $brand-primary-light;
     border-bottom: 1px solid $color-alto;
 
     .panel-title > a {
@@ -729,8 +729,8 @@ ul.content-module-activities {
 
     .activity-item-date {
       font-size: 1.2em;
-      background-color: $color-theme-primary;
-      border-color: $color-theme-primary;
+      background-color: $brand-primary;
+      border-color: $brand-primary;
       color: $color-white;
       padding-top: 5px;
       padding-bottom: 5px;
@@ -898,16 +898,17 @@ ul.content-module-activities {
 
 .dnd-error,
 .dnd-total-error {
-  color: $color-milano-red;
+  color: $brand-danger;
 }
 
 .is-dragover {
-  background: $color-drag-overlay;
+  background: $color-black;
   bottom: 0;
   display: none;
   height: 100%;
   left: 0;
   min-height: 100%;
+  opacity: .4;
   pointer-events: none;
   position: fixed;
   right: 0;
@@ -995,7 +996,7 @@ table.dataTable {
   word-break: initial;
 
   thead {
-    background-color: $color-gray;
+    background-color: $color-silver-chalice;
   }
 
   thead > tr > th {
@@ -1020,13 +1021,13 @@ table.dataTable {
     color: $color-emperor !important;
 
     a {
-      color: $color-theme-primary !important;
+      color: $brand-primary !important;
     }
   }
 
   .sorting_desc,
   .sorting_asc {
-    background-color: $color-theme-primary;
+    background-color: $brand-primary;
   }
 }
 
@@ -1067,12 +1068,12 @@ table.dataTable {
     top: 50%;
     margin-top: -19px;
     border-top: 19px solid transparent;
-    border-left: 13px solid $color-theme-primary;
+    border-left: 13px solid $brand-primary;
     border-bottom: 19px solid transparent;
 }
 
 .nav-stacked-arrow > li.active > a:hover:after {
-  border-left: 13px solid darken($color-theme-primary, 15%);
+  border-left: 13px solid darken($brand-primary, 15%);
 }
 
 /* Overlay to disable interaction while loading ajax */
@@ -1094,7 +1095,7 @@ table.dataTable {
 }
 
 .turbolinks-progress-bar::before {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
 }
 
 /* Loading animation for ajax events, inspired by Codrops */
@@ -1105,7 +1106,7 @@ table.dataTable {
   z-index: -1;
   width: 100%;
   height: 3px;
-  background: $color-theme-primary;
+  background: $brand-primary;
   -webkit-transform: translate3d(-100%, 0, 0);
   transform: translate3d(-100%, 0, 0);
   pointer-events: none;
@@ -1136,7 +1137,7 @@ table.dataTable {
 
 .custom .introjs-skipbutton {
   border-radius: 0;
-  color: $color-theme-primary;
+  color: $brand-primary;
   background-color: $color-white;
   background-image: none;
   border: none;
@@ -1162,7 +1163,7 @@ table.dataTable {
   .modal-tooltiptext {
     background-color: $color-alto;
     border-radius: 6px;
-    color: $color-mine-shaft;
+    color: $color-emperor;
     display: block;
     margin-left: 100px;
     padding: 5px;
@@ -1204,7 +1205,7 @@ table.dataTable {
   top: auto;
 
   li:not(.dropdown-header):hover {
-    background-color: $color-wild-sand;
+    background-color: $color-concrete;
   }
 }
 
@@ -1479,7 +1480,7 @@ textarea.textarea-sm {
     }
 
     .ok {
-      color: $color-theme-secondary;
+      color: $brand-default;
       margin-right: 5px;
     }
 
@@ -1533,7 +1534,7 @@ th.custom-field .modal-tooltiptext {
   color: $color-black;
   border: 1px solid $color-emperor;
   border-radius: 3px;
-  box-shadow: 0 0 5px $color-cloud;
+  box-shadow: 0 0 5px $color-gainsboro;
   min-width: 520px;
   max-height: 200px;
   overflow: auto;
@@ -1546,11 +1547,11 @@ th.custom-field .modal-tooltiptext {
   }
 
   strong {
-    color: $color-theme-primary;
+    color: $brand-primary;
   }
 
   .cur {
-    background: $color-theme-primary;
+    background: $brand-primary;
     color: $color-white;
 
     small {
@@ -1582,7 +1583,7 @@ th.custom-field .modal-tooltiptext {
   padding-top: 3px;
   padding-bottom: 7px;
   height: 34px;
-  background-color: $color-gallery;
+  background-color: $color-concrete;
   border-bottom: 1px solid $color-emperor;
   clear: both;
 
diff --git a/app/javascript/src/styles/constants.scss b/app/javascript/src/styles/constants.scss
index f7c6b8b65..1e3475eca 100644
--- a/app/javascript/src/styles/constants.scss
+++ b/app/javascript/src/styles/constants.scss
@@ -3,50 +3,24 @@
 //==============================================================================
 
 // Theme colors
-$color-theme-primary: #37a0d9;
-$color-theme-secondary: #8fd13f;
-$color-theme-dark: #6d6e71;
+$brand-primary: #37a0d9;
+$brand-default: #8fd13f;
 
 // Grayscale colors
 $color-white: #fff;
 $color-alabaster: #fcfcfc;
-$color-snow: #f9f9f9;
-$color-wild-sand: #f5f5f5;
 $color-concrete: #f2f2f2;
-$color-gallery: #eee;
 $color-gainsboro: #e3e3e3;
 $color-alto: #d2d2d2;
 $color-silver: #c5c5c5;
-$color-dark-gray: #adadad;
 $color-silver-chalice: #a0a0a0;
-$color-gray: #909088;
 $color-dove-gray: #666;
 $color-emperor: #555;
-$color-mine-shaft: #333;
-$color-nero: #262626;
 $color-black: #000;
-$color-cloud: rgba(0, 0, 0, .1);
-$color-gray-light-yadcf: #ccc;
-$color-gray-dark-yadcf: #a9a9a9;
 
 // Miscelaneous colors
-$color-mystic: #eaeff2;
-$color-candlelight: #ffda23;
-$color-orange: #ff900b;
-$color-saturated-green: #008600;
-$color-blue-yadcf: #337ab7;
 $primary-hover-color: #75b22b;
 
-// Red colors
-$color-mojo: #cf4b48;
-$color-apple-blossom: #a94442;
-$color-milano-red: #a70b05;
-
-// Colors for specific intents
-$color-visited-link: #23527c;
-
-// Overlay shade for drag'n dropdown
-$color-drag-overlay: rgba(0, 0, 0, .4);
 
 //==============================================================================
 // Other
diff --git a/app/javascript/src/styles/main.scss b/app/javascript/src/styles/main.scss
index fa4d592e1..8b9f89f68 100644
--- a/app/javascript/src/styles/main.scss
+++ b/app/javascript/src/styles/main.scss
@@ -9,7 +9,7 @@ body {
 }
 
 .label-primary {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
 }
 
 .btn {
@@ -17,18 +17,18 @@ body {
 }
 
 .btn-primary {
-  background-color: $color-theme-secondary;
-  border-color: darken($color-theme-secondary, 5%);
+  background-color: $brand-default;
+  border-color: darken($brand-default, 5%);
 
   &.active,
   &.focus,
   &.active.focus {
-    background-color: darken($color-theme-secondary, 20%);
-    border-color: darken($color-theme-secondary, 25%);
+    background-color: darken($brand-default, 20%);
+    border-color: darken($brand-default, 25%);
 
     &:hover {
-      background-color: darken($color-theme-secondary, 25%);
-      border-color: darken($color-theme-secondary, 30%);
+      background-color: darken($brand-default, 25%);
+      border-color: darken($brand-default, 30%);
     }
   }
 
@@ -38,19 +38,19 @@ body {
   &:active:hover,
   &:focus:hover,
   &:active:focus:hover {
-    background-color: darken($color-theme-secondary, 20%);
-    border-color: darken($color-theme-secondary, 25%);
+    background-color: darken($brand-default, 20%);
+    border-color: darken($brand-default, 25%);
   }
 
   &:hover {
-    background-color: darken($color-theme-secondary, 5%);
-    border-color: darken($color-theme-secondary, 10%);
+    background-color: darken($brand-default, 5%);
+    border-color: darken($brand-default, 10%);
   }
 }
 
 // tags input
 .react-tagsinput--focused {
-  border-color: $color-theme-primary;
+  border-color: $brand-primary;
 }
 
 .react-tagsinput-input {
@@ -58,7 +58,7 @@ body {
 }
 
 .react-tagsinput-tag {
-  background-color: $color-theme-primary;
+  background-color: $brand-primary;
   border: 0;
   color: $color-white;
   font-weight: bold;
diff --git a/config/initializers/constants.rb b/config/initializers/constants.rb
index 4fdbbc1a6..5af86d880 100644
--- a/config/initializers/constants.rb
+++ b/config/initializers/constants.rb
@@ -144,40 +144,21 @@ class Constants
   ].freeze
 
   # Theme colors
-  COLOR_THEME_PRIMARY = '#37a0d9'.freeze # $color-theme-primary
-  COLOR_THEME_SECONDARY = '#8fd13f'.freeze # $color-theme-secondary
-  COLOR_THEME_DARK = '#6d6e71'.freeze # $color-theme-dark
+  COLOR_THEME_PRIMARY = '#37a0d9'.freeze # $brand-primary
+  COLOR_THEME_SECONDARY = '#8fd13f'.freeze # $brand-default
 
   # Grayscale colors
   COLOR_WHITE = '#ffffff'.freeze # $color-white
   COLOR_ALABASTER = '#fcfcfc'.freeze # $color-alabaster
-  COLOR_SNOW = '#f9f9f9'.freeze # $color-snow
-  COLOR_WILD_SAND = '#f5f5f5'.freeze # $color-wild-sand
   COLOR_CONCRETE = '#f2f2f2'.freeze # $color-concrete
-  COLOR_GALLERY = '#eeeeee'.freeze # $color-gallery
   COLOR_GAINSBORO = '#e3e3e3'.freeze # $color-gainsboro
   COLOR_ALTO = '#d2d2d2'.freeze # $color-alto
   COLOR_SILVER = '#c5c5c5'.freeze # $color-silver
-  COLOR_DARK_GRAY = '#adadad'.freeze # $color-dark-gray
   COLOR_SILVER_CHALICE = '#a0a0a0'.freeze # $color-silver-chalice
-  COLOR_GRAY = '#909088'.freeze # $color-gray
   COLOR_DOVE_GRAY = '#666666'.freeze # $color-dove-gray
   COLOR_EMPEROR = '#555555'.freeze # $color-emperor
-  COLOR_MINE_SHAFT = '#333333'.freeze # $color-mine-shaft
-  COLOR_NERO = '#262626'.freeze # $color-nero
   COLOR_BLACK = '#000000'.freeze # $color-black
-  COLOR_GRAY_LIGHT_YADCF = '#cccccc'.freeze # $color-gray-light-yadcf
-  COLOR_GRAY_DARK_YADCF = '#a9a9a9'.freeze # $color-gray-dark-yadcf
-
-  # Miscelaneous colors
-  COLOR_MYSTIC = '#eaeff2'.freeze # $color-mystic
-  COLOR_CANDLELIGHT = '#ffda23'.freeze # $color-candlelight
-  COLOR_BLUE_YADCF = '#337ab7'.freeze # $color-blue-yadcf
-
-  # Red colors
-  COLOR_MOJO = '#cf4b48'.freeze # $color-mojo
-  COLOR_APPLE_BLOSSOM = '#a94442'.freeze # $color-apple-blossom
-  COLOR_MILANO_RED = '#a70b05'.freeze # $color-milano-red
+  
 
   #=============================================================================
   # External URLs

From 7c1390ece2d81219cb0a9c9359e59bafbcf8f3f9 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 28 Mar 2018 14:12:11 +0200
Subject: [PATCH 06/23] implement sidebar toggle [fixes SCI-2232]

---
 app/assets/javascripts/application.js.erb    |  1 +
 app/assets/javascripts/sidebar_toggle.js.erb | 35 ++++++++++++++++++++
 app/controllers/repositories_controller.rb   |  2 +-
 app/views/repositories/_sidebar.html.erb     | 29 ++++++++++------
 app/views/shared/_left_menu_bar.html.erb     | 19 +++++++++--
 app/views/shared/_sidebar.html.erb           |  1 -
 config/initializers/assets.rb                |  1 +
 7 files changed, 73 insertions(+), 15 deletions(-)
 create mode 100644 app/assets/javascripts/sidebar_toggle.js.erb

diff --git a/app/assets/javascripts/application.js.erb b/app/assets/javascripts/application.js.erb
index 167546640..10d795c56 100644
--- a/app/assets/javascripts/application.js.erb
+++ b/app/assets/javascripts/application.js.erb
@@ -12,6 +12,7 @@
 //= require jquery-ui/widgets/draggable
 //= require jquery-ui/widgets/droppable
 //= require jquery.ui.touch-punch.min
+//= require jquery-ui/effects/effect-slide
 //= require jquery.caret.min
 //= require jquery.atwho.min
 //= require hammer
diff --git a/app/assets/javascripts/sidebar_toggle.js.erb b/app/assets/javascripts/sidebar_toggle.js.erb
new file mode 100644
index 000000000..6084d4c3d
--- /dev/null
+++ b/app/assets/javascripts/sidebar_toggle.js.erb
@@ -0,0 +1,35 @@
+(function(global) {
+  'use strict';
+  global.SideBarToggle = (function() {
+
+    function show() {
+      $('#sideBarLeft').show();
+      $('#sideBarRight').hide();
+      $('#sidebar-wrapper').show(
+        'slide', { direction: 'right', easing: 'linear' }, 400
+      );
+      $('#wrapper').css('paddingLeft', '280px');
+      $('.navbar-secondary').css(
+        { 'margin-left': '-280px', 'padding-left': '280px' }
+      );
+    }
+
+    function hide() {
+      $('#sideBarLeft').hide();
+      $('#sideBarRight').show();
+      $('#sidebar-wrapper').hide(
+        'slide', { direction: 'left', easing: 'linear'}, 400
+      );
+      $('#wrapper').css('paddingLeft', '0');
+      $('.navbar-secondary').css({
+        'margin-left': '0',
+        'padding-left': '0'
+      });
+    }
+
+    return Object.freeze({
+      show: show,
+      hide: hide
+    })
+  })();
+})(window);
diff --git a/app/controllers/repositories_controller.rb b/app/controllers/repositories_controller.rb
index d0351a324..cb8bd4d09 100644
--- a/app/controllers/repositories_controller.rb
+++ b/app/controllers/repositories_controller.rb
@@ -11,7 +11,7 @@ class RepositoriesController < ApplicationController
   before_action :check_create_permissions, only:
     %i(create_new_modal create copy_modal copy)
 
-  # layout 'fluid'
+  layout 'fluid'
 
   def index
     unless @repositories.length.zero? && current_team
diff --git a/app/views/repositories/_sidebar.html.erb b/app/views/repositories/_sidebar.html.erb
index 273fd0f17..e5fa31153 100644
--- a/app/views/repositories/_sidebar.html.erb
+++ b/app/views/repositories/_sidebar.html.erb
@@ -1,23 +1,30 @@
  <%= content_for :sidebar do %>
   <div id="slide-panel" class="visible">
-    <div class="sidebar-header">
-      <div class="sidebar-header-title">
-        <h5><%=t "libraries.sidebar.title" %></h5>
-      </div>
-    </div>
-    <div class="sidebar-header-toggle">
-      <a href="" id="toggle-sidebar-link">
-        <span class="glyphicon glyphicon-play-circle"></span>
-      </a>
-    </div>
     <div class="tree">
       <ul>
+        <li>
+          <span class="tree-link line-wrap no-indent">
+            <strong title="<%= t('libraries.sidebar.title') %>"><%= t('libraries.sidebar.title') %></strong>
+          </span>
+        </li>
         <% repositories.each do |repository| %>
           <% cache repository do %>
-            <li><%= link_to repository.name, repository_path(repository) %></li>
+            <li class="<%= 'active' if current_page?(repository_path(repository)) %>" >
+              <span class="tree-link line-wrap no-indent">
+                <%= link_to repository.name,
+                            repository_path(repository),
+                            data: { 'no-turbolink' => 'true' } %>
+              </span>
+            </li>
           <% end %>
         <% end %>
       </ul>
     </div>
   </div>
 <% end %>
+
+<script>
+  $(document).ready(function() {
+    $('#wrapper').show();
+  })
+</script>
diff --git a/app/views/shared/_left_menu_bar.html.erb b/app/views/shared/_left_menu_bar.html.erb
index b65ac952e..457acf415 100644
--- a/app/views/shared/_left_menu_bar.html.erb
+++ b/app/views/shared/_left_menu_bar.html.erb
@@ -1,13 +1,26 @@
 <div id="left-menu-bar" class="menu-bar">
   <ul class="nav">
+    <li class="text-center">
+      <span id="sideBarLeft"
+            class="glyphicon glyphicon-chevron-left"
+            aria-hidden="true"
+            onclick="SideBarToggle.hide()"
+            ></span>
+      <span id="sideBarRight"
+            class="glyphicon glyphicon-chevron-right"
+            aria-hidden="true"
+            onclick="SideBarToggle.show()"
+            style="display:none;"
+            ></span>
+    </li>
     <li class="<%= "active" if projects_are_selected? %>">
-      <%= link_to projects_path, id: "projects-link", class: "toggle-sidebar-link", title: t('left_menu_bar.projects') do %>
+      <%= link_to projects_path, id: "projects-link", title: t('left_menu_bar.projects') do %>
         <span class="glyphicon glyphicon-home"></span>
         <span><%= t('left_menu_bar.projects') %></span>
       <% end %>
     </li>
     <li class="<%= "active" if repositories_are_selected? %>">
-      <%= link_to team_repositories_path(current_team), id: "repositories-link", title: t('left_menu_bar.repositories') do %>
+      <%= link_to repositories_path, id: "repositories-link", title: t('left_menu_bar.repositories') do %>
         <span class="fa fa-cubes" aria-hidden="true"></span>
         <span><%= t('left_menu_bar.repositories') %></span>
       <% end %>
@@ -65,3 +78,5 @@
     </li>
   </ul>
 </div>
+
+<%= javascript_include_tag("sidebar_toggle") %>
diff --git a/app/views/shared/_sidebar.html.erb b/app/views/shared/_sidebar.html.erb
index 6069cdf2f..d1f177c5e 100644
--- a/app/views/shared/_sidebar.html.erb
+++ b/app/views/shared/_sidebar.html.erb
@@ -1,6 +1,5 @@
 <%= content_for :sidebar do %>
   <div id="slide-panel" class="visible">
-
     <div class="tree">
       <ul>
         <% if project_page? && action_name == 'index' ||
diff --git a/config/initializers/assets.rb b/config/initializers/assets.rb
index 38f4189e9..537dbec35 100644
--- a/config/initializers/assets.rb
+++ b/config/initializers/assets.rb
@@ -84,6 +84,7 @@ Rails.application.config.assets.precompile +=
   %w(repositories/my_module_repository.js)
 Rails.application.config.assets.precompile += %w(activities/index.js)
 Rails.application.config.assets.precompile += %w(repositories/show.js)
+Rails.application.config.assets.precompile += %w(sidebar_toggle.js)
 
 # Libraries needed for Handsontable formulas
 Rails.application.config.assets.precompile += %w(lodash.js)

From 4bf9369bc59bfe5b7da2d51985743ee5134c87bb Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Thu, 29 Mar 2018 13:58:14 +0200
Subject: [PATCH 07/23] refactor buttons

---
 app/assets/javascripts/protocols/steps.js.erb |   2 +-
 app/assets/stylesheets/constants.scss         | 104 ++++++++--------
 app/assets/stylesheets/notifications.scss     |  19 +--
 .../stylesheets/protocol_management.scss      |  20 +++
 app/assets/stylesheets/settings.scss          |   3 +
 app/assets/stylesheets/themes/buttons.scss    | 114 ------------------
 .../stylesheets/themes/main_navigation.scss   |  23 ----
 app/assets/stylesheets/themes/scinote.scss    |  24 ++--
 .../_state_button_uncomplete.html.erb         |   2 +-
 app/views/my_modules/results.html.erb         |   4 +-
 app/views/protocols/_steps.html.erb           |   4 +-
 app/views/user_notifications/index.html.erb   |  10 +-
 app/views/users/registrations/edit.html.erb   |   2 +-
 13 files changed, 100 insertions(+), 231 deletions(-)
 create mode 100644 app/assets/stylesheets/protocol_management.scss
 create mode 100644 app/assets/stylesheets/settings.scss
 delete mode 100644 app/assets/stylesheets/themes/buttons.scss

diff --git a/app/assets/javascripts/protocols/steps.js.erb b/app/assets/javascripts/protocols/steps.js.erb
index adefb94b1..69fe217a0 100644
--- a/app/assets/javascripts/protocols/steps.js.erb
+++ b/app/assets/javascripts/protocols/steps.js.erb
@@ -43,7 +43,7 @@
             var task_button = $("[data-action='complete-task']");
             task_button.attr('data-action', 'uncomplete-task');
             task_button.find('.btn')
-              .removeClass('btn-primary').addClass('btn-greyed');
+              .removeClass('btn-primary').addClass('btn-default');
             $('.task-due-date').html(data.module_header_due_date_label);
             $('.task-state-label').html(data.module_state_label);
             task_button
diff --git a/app/assets/stylesheets/constants.scss b/app/assets/stylesheets/constants.scss
index 8e0c00d85..8404a75b0 100644
--- a/app/assets/stylesheets/constants.scss
+++ b/app/assets/stylesheets/constants.scss
@@ -48,12 +48,12 @@ $gray: $color-emperor;
 $gray-light: $color-dove-gray;
 $gray-lighter: $color-concrete;
 
-// // Scaffolding
-// $body-bg: #fff;
-// $text-color: #ee3df0;
-// $link-color: $brand-primary;
-// $link-hover-color: darken($link-color, 15%);
-// $link-hover-decoration: underline;
+// Scaffolding
+$body-bg: $color-white;
+$text-color: $gray-dark;
+$link-color: $brand-primary;
+$link-hover-color: darken($link-color, 15%);
+$link-hover-decoration: underline;
 
 // // Typography
 // $font-family-sans-serif: "Open Sans", Arial, Helvetica, sans-serif;
@@ -80,26 +80,26 @@ $gray-lighter: $color-concrete;
 // $icon-font-path: "../fonts/";
 // $icon-font-name: "glyphicons-halflings-regular";
 // $icon-font-svg-id: "glyphicons_halflingsregular";
-//
-// // Components
-// $padding-base-vertical: 6px;
-// $padding-base-horizontal: 12px;
-// $padding-large-vertical: 10px;
-// $padding-large-horizontal: 16px;
-// $padding-small-vertical: 5px;
-// $padding-small-horizontal: 10px;
-// $padding-xs-vertical: 1px;
-// $padding-xs-horizontal: 5px;
-// $line-height-large: 1.3333333;
-// $line-height-small: 1.5;
-// $border-radius-base: 4px;
-// $border-radius-large: 6px;
-// $border-radius-small: 3px;
-// $component-active-color: #fff;
-// $component-active-bg: $brand-primary;
-// $caret-width-base: 4px;
-// $caret-width-large: 5px;
-//
+
+// Components
+$padding-base-vertical: 6px;
+$padding-base-horizontal: 12px;
+$padding-large-vertical: 10px;
+$padding-large-horizontal: 16px;
+$padding-small-vertical: 5px;
+$padding-small-horizontal: 10px;
+$padding-xs-vertical: 1px;
+$padding-xs-horizontal: 5px;
+$line-height-large: 1.3333333;
+$line-height-small: 1.5;
+$border-radius-base: 4px;
+$border-radius-large: 6px;
+$border-radius-small: 3px;
+$component-active-color: $color-white;
+$component-active-bg: $brand-primary;
+$caret-width-base: 4px;
+$caret-width-large: 5px;
+
 // // Tables
 // $table-cell-padding: 8px;
 // $table-condensed-cell-padding: 5px;
@@ -108,32 +108,32 @@ $gray-lighter: $color-concrete;
 // $table-bg-hover: #f5f5f5;
 // $table-bg-active: $table-bg-hover;
 // $table-border-color: #ddd;
-//
-// // Buttons
-// $btn-font-weight: normal;
-// $btn-default-color: #333;
-// $btn-default-bg: $brand-default;
-// $btn-default-border: #ccc;
-// $btn-primary-color: #fff;
-// $btn-primary-bg: $brand-primary;
-// $btn-primary-border: darken($btn-primary-bg, 5%);
-// $btn-success-color: #fff;
-// $btn-success-bg: $brand-success;
-// $btn-success-border: darken($btn-success-bg, 5%);
-// $btn-info-color: #fff;
-// $btn-info-bg: $brand-info;
-// $btn-info-border: darken($btn-info-bg, 5%);
-// $btn-warning-color: #fff;
-// $btn-warning-bg: $brand-warning;
-// $btn-warning-border: darken($btn-warning-bg, 5%);
-// $btn-danger-color: #fff;
-// $btn-danger-bg: $brand-danger;
-// $btn-danger-border: darken($btn-danger-bg, 5%);
-// $btn-link-disabled-color: $gray-light;
-// $btn-border-radius-base: $border-radius-base;
-// $btn-border-radius-large: $border-radius-large;
-// $btn-border-radius-small: $border-radius-small;
-//
+
+// Buttons
+$btn-font-weight: normal;
+$btn-default-color: $gray-dark;
+$btn-default-bg: $brand-default;
+$btn-default-border: $color-silver;
+$btn-primary-color: $color-white;
+$btn-primary-bg: $brand-primary;
+$btn-primary-border: darken($btn-primary-bg, 5%);
+$btn-success-color: $color-white;
+$btn-success-bg: $brand-success;
+$btn-success-border: darken($btn-success-bg, 5%);
+$btn-info-color: $color-white;
+$btn-info-bg: $brand-info;
+$btn-info-border: darken($btn-info-bg, 5%);
+$btn-warning-color: $color-white;
+$btn-warning-bg: $brand-warning;
+$btn-warning-border: darken($btn-warning-bg, 5%);
+$btn-danger-color: $color-white;
+$btn-danger-bg: $brand-danger;
+$btn-danger-border: darken($btn-danger-bg, 5%);
+$btn-link-disabled-color: $gray-light;
+$btn-border-radius-base: $border-radius-base;
+$btn-border-radius-large: $border-radius-large;
+$btn-border-radius-small: $border-radius-small;
+
 // // Forms
 // $input-bg: #fff;
 // $input-bg-disabled: $gray-lighter;
diff --git a/app/assets/stylesheets/notifications.scss b/app/assets/stylesheets/notifications.scss
index 9ef0f991b..68e27dbf9 100644
--- a/app/assets/stylesheets/notifications.scss
+++ b/app/assets/stylesheets/notifications.scss
@@ -82,21 +82,6 @@
   }
 }
 
-
-.notifications-footer {
-
-  background-color: $brand-primary-light;
-
-  .btn-more-notifications {
-    border-bottom: 1px solid $color-alto;
-    border-left: 1px solid $color-alto;
-    border-right: 1px solid $color-alto;
-    margin: 0;
-    padding: 8px;
-    text-align: center;
-
-    &:hover {
-      background-color: $brand-primary-light;
-    }
-  }
+.btn-more-notifications {
+  margin-top: 15px;
 }
diff --git a/app/assets/stylesheets/protocol_management.scss b/app/assets/stylesheets/protocol_management.scss
new file mode 100644
index 000000000..08d973e37
--- /dev/null
+++ b/app/assets/stylesheets/protocol_management.scss
@@ -0,0 +1,20 @@
+.btn-open-file {
+  position: relative;
+  overflow: hidden;
+
+  & > input[type=file] {
+    position: absolute;
+    top: 0;
+    right: 0;
+    min-width: 100%;
+    min-height: 100%;
+    font-size: 100px;
+    text-align: right;
+    filter: alpha(opacity=0);
+    opacity: 0;
+    outline: none;
+    background: white;
+    cursor: inherit;
+    display: block;
+  }
+}
diff --git a/app/assets/stylesheets/settings.scss b/app/assets/stylesheets/settings.scss
new file mode 100644
index 000000000..002b244eb
--- /dev/null
+++ b/app/assets/stylesheets/settings.scss
@@ -0,0 +1,3 @@
+#reset-tutorial-btn {
+  margin-top: 5px;
+}
diff --git a/app/assets/stylesheets/themes/buttons.scss b/app/assets/stylesheets/themes/buttons.scss
deleted file mode 100644
index 447837728..000000000
--- a/app/assets/stylesheets/themes/buttons.scss
+++ /dev/null
@@ -1,114 +0,0 @@
-@import 'constants';
-@import "mixins";
-
-
-#reset-tutorial-btn {
-  margin-top: 15px;
-}
-
-.btn-primary {
-  background-color: $color-theme-secondary;
-  border-color: darken($color-theme-secondary, 5%);
-
-  &.active,
-  &.focus,
-  &.active.focus {
-    background-color: darken($color-theme-secondary, 20%);
-    border-color: darken($color-theme-secondary, 25%);
-
-    &:hover {
-      background-color: darken($color-theme-secondary, 25%);
-      border-color: darken($color-theme-secondary, 30%);
-    }
-  }
-
-  &:active,
-  &:focus,
-  &:active:focus,
-  &:active:hover,
-  &:focus:hover,
-  &:active:focus:hover {
-    background-color: darken($color-theme-secondary, 20%);
-    border-color: darken($color-theme-secondary, 25%);
-  }
-
-  &:hover {
-    background-color: darken($color-theme-secondary, 5%);
-    border-color: darken($color-theme-secondary, 10%);
-  }
-}
-.btn-link-alt {
-  border-radius: 4px;
-  cursor: pointer;
-  margin-right: 5px;
-  padding: 3px;
-}
-
-.btn-invis-file {
-  display: none;
-  opacity: 0;
-  position: absolute;
-  z-index: -1;
-}
-
-.btn-open-file {
-  position: relative;
-  overflow: hidden;
-
-  & > input[type=file] {
-    position: absolute;
-    top: 0;
-    right: 0;
-    min-width: 100%;
-    min-height: 100%;
-    font-size: 100px;
-    text-align: right;
-    filter: alpha(opacity=0);
-    opacity: 0;
-    outline: none;
-    background: white;
-    cursor: inherit;
-    display: block;
-  }
-}
-
-/** Add users modal  */
-.btn-group-existing-users {
-  width: 100%;
-
-  label.btn {
-    text-align: center;
-
-    &.btn-title {
-      color: $color-white;
-      cursor: inherit;
-      background-color: $color-theme-primary;
-
-      &:focus, &:active, &:hover {
-        box-shadow: none;
-        background-color: $color-theme-primary;
-        border-color: $color-dark-gray;
-      }
-    }
-  }
-}
-
-.btn-greyed {
-  background-color: $color-silver-chalice;
-  border-color: $color-silver-chalice;
-  color: $color-white;
-
-  &:hover,
-  &:focus {
-    background-color: darken($color-silver-chalice, 15%);
-    border-color: darken($color-silver-chalice, 15%);
-    color: $color-white;
-  }
-}
-
-/* Sample group color picker */
-.btn-group-sample-group-color {
-  .btn-group > .btn {
-    border-radius: 0 !important;
-  }
-}
diff --git a/app/assets/stylesheets/themes/main_navigation.scss b/app/assets/stylesheets/themes/main_navigation.scss
index 903bf6744..a5f177bd1 100644
--- a/app/assets/stylesheets/themes/main_navigation.scss
+++ b/app/assets/stylesheets/themes/main_navigation.scss
@@ -157,21 +157,6 @@
   padding-left: 45px;
 }
 
-#search-bar {
-  border-color: $color-alto;
-  .btn-default {
-    background-color: $brand-primary;
-    border-color: $brand-primary;
-    color: $color-white;
-  }
-
-  input {
-    border-bottom-left-radius: 0;
-    border-top-left-radius: 0;
-    width: 300px;
-  }
-}
-
 /** Search */
 .nav-search {
   li.disabled {
@@ -286,22 +271,14 @@
   }
 
   .btn-default {
-    border-bottom-left-radius: 0;
-    border-top-left-radius: 0;
     text-align: right;
     width: 300px;
   }
 
   .btn-group {
-    border-color: $color-alto;
     margin-top: 8px;
   }
 
-  .btn-primary {
-    background-color: $brand-primary;
-    border-color: $brand-primary;
-  }
-
   .dropdown-menu {
     width: 100%;
   }
diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss
index 07004b8e2..00245ed39 100644
--- a/app/assets/stylesheets/themes/scinote.scss
+++ b/app/assets/stylesheets/themes/scinote.scss
@@ -1,7 +1,6 @@
 @import 'constants';
 @import "mixins";
 @import "main_navigation";
-@import "buttons";
 
 /** Layout **/
 
@@ -1241,9 +1240,19 @@ table.dataTable {
   position: absolute;
   z-index: 10;
 
-  .btn-greyed {
+  .btn-grey {
+    background-color: $color-silver-chalice;
+    border-color: $color-silver-chalice;
     border-radius: 0;
+    color: $color-white;
     width: 100px;
+
+    &:hover,
+    &:focus {
+      background-color: darken($color-silver-chalice, 15%);
+      border-color: darken($color-silver-chalice, 15%);
+      color: $color-white;
+    }
   }
 }
 
@@ -1386,15 +1395,6 @@ textarea.textarea-sm {
       -webkit-padding-before: 0;
       -webkit-padding-after: 0;
     }
-    .btn.btn-default-link {
-      border: 0;
-      height: 100%;
-      min-height: 34px;
-      padding: 0;
-      -webkit-padding-after: 0;
-      -webkit-padding-before: 0;
-    }
-
   }
 }
 
@@ -1596,12 +1596,10 @@ th.custom-field .modal-tooltiptext {
     margin-left: 15px;
 
     .btn {
-      border-radius: 4px;
       margin-right: 5px;
       padding: 3px;
     }
 
-
     .btn:last-child {
       margin-right: 20px;
     }
diff --git a/app/views/my_modules/_state_button_uncomplete.html.erb b/app/views/my_modules/_state_button_uncomplete.html.erb
index 86805dbf2..7c06d4f8e 100644
--- a/app/views/my_modules/_state_button_uncomplete.html.erb
+++ b/app/views/my_modules/_state_button_uncomplete.html.erb
@@ -1,4 +1,4 @@
-<button class="btn btn-greyed">
+<button class="btn btn-default">
   <span class="glyphicon glyphicon-remove"></span>
   <%= t("my_modules.buttons.uncomplete") %>
 </button>
\ No newline at end of file
diff --git a/app/views/my_modules/results.html.erb b/app/views/my_modules/results.html.erb
index b33102229..0243b15b4 100644
--- a/app/views/my_modules/results.html.erb
+++ b/app/views/my_modules/results.html.erb
@@ -5,10 +5,10 @@
 
 <div id="results-toolbar">
   <div class="pull-right">
-    <button class="btn btn-greyed" id="results-collapse-btn">
+    <button class="btn btn-default" id="results-collapse-btn">
       <span class="glyphicon glyphicon-collapse-up"></span>
       <span class="hidden-xs-custom"><%= t'my_modules.results.collapse_label' %></button></span>
-    <button class="btn btn-greyed" id="results-expand-btn">
+    <button class="btn btn-default" id="results-expand-btn">
       <span class="glyphicon glyphicon-collapse-down"></span>
       <span class="hidden-xs-custom"><%= t'my_modules.results.expand_label' %></button></span>
   </div>
diff --git a/app/views/protocols/_steps.html.erb b/app/views/protocols/_steps.html.erb
index bb059225c..8ecf43146 100644
--- a/app/views/protocols/_steps.html.erb
+++ b/app/views/protocols/_steps.html.erb
@@ -10,10 +10,10 @@
         <span class="hidden-xs"><%=t "protocols.steps.new_step" %></span>
       </a>
     <% end %>
-    <a class="btn btn-greyed" data-action="collapse-steps">
+    <a class="btn btn-default" data-action="collapse-steps">
       <span class="glyphicon glyphicon-collapse-up"></span>
       <span class="hidden-xs"><%= t("protocols.steps.collapse_label") %></a></span>
-    <a class="btn btn-greyed" data-action="expand-steps">
+    <a class="btn btn-default" data-action="expand-steps">
       <span class="glyphicon glyphicon-collapse-down"></span>
       <span class="hidden-xs"><%= t("protocols.steps.expand_label") %></a></span>
   </div>
diff --git a/app/views/user_notifications/index.html.erb b/app/views/user_notifications/index.html.erb
index c8ceac8fb..6cfbefdbd 100644
--- a/app/views/user_notifications/index.html.erb
+++ b/app/views/user_notifications/index.html.erb
@@ -14,13 +14,13 @@
       <% end %>
     </ul>
   </div>
-  <div class="notifications-footer">
     <% if @overflown %>
-      <a class="btn-more-notifications col-xs-12" href="<%= @more_notifications_url %>" data-remote="true">
-        <span><%= t('notifications.show_more') %></span>
-      </a>
+      <div class="text-center">
+        <a class="btn btn-default btn-more-notifications" href="<%= @more_notifications_url %>" data-remote="true">
+          <span><%= t('notifications.show_more') %></span>
+        </a>
+      </div>
     <% end %>
-  </div>
 </div>
 
 <%= javascript_include_tag("notifications") %>
diff --git a/app/views/users/registrations/edit.html.erb b/app/views/users/registrations/edit.html.erb
index c27d23e93..6ac1bd0d9 100644
--- a/app/views/users/registrations/edit.html.erb
+++ b/app/views/users/registrations/edit.html.erb
@@ -33,7 +33,7 @@
                         <%= image_tag @user_avatar_url %>
                       </div>
                       <div class="avatar-edit">
-                        <div class="btn btn-greyed btn-sm">
+                        <div class="btn btn-grey btn-sm">
                           <span class="glyphicon glyphicon-pencil"></span>
                           <%=t "users.registrations.edit.avatar_btn" %>
                         </div>

From 659a088058437821f57b94208aab918ac33a5dd9 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Thu, 29 Mar 2018 15:55:26 +0200
Subject: [PATCH 08/23] refactor smart annotation parser, adds repository item
 to smart annotation parser [fixes SCI-2222]

---
 app/helpers/application_helper.rb             | 63 +--------------
 app/permissions/project.rb                    |  1 -
 .../smart_annotations/permision_eval.rb       | 35 +++++++++
 app/services/smart_annotations/preview.rb     | 77 +++++++++++++++++++
 app/services/smart_annotations/tag_to_html.rb | 66 ++++++++++++++++
 .../smart_annotations/permission_eval_spec.rb | 47 +++++++++++
 .../smart_annotations/preview_spec.rb         | 63 +++++++++++++++
 .../smart_annotations/tag_to_html_spec.rb     | 44 +++++++++++
 8 files changed, 333 insertions(+), 63 deletions(-)
 create mode 100644 app/services/smart_annotations/permision_eval.rb
 create mode 100644 app/services/smart_annotations/preview.rb
 create mode 100644 app/services/smart_annotations/tag_to_html.rb
 create mode 100644 spec/services/smart_annotations/permission_eval_spec.rb
 create mode 100644 spec/services/smart_annotations/preview_spec.rb
 create mode 100644 spec/services/smart_annotations/tag_to_html_spec.rb

diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 59dc86689..cb7c7b3ac 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -117,68 +117,7 @@ module ApplicationHelper
   # Check if text have smart annotations of resources
   # and outputs a link to resource
   def smart_annotation_filter_resources(text)
-    sa_reg = /\[\#(.*?)~(prj|exp|tsk|sam)~([0-9a-zA-Z]+)\]/
-    new_text = text.gsub(sa_reg) do |el|
-      match = el.match(sa_reg)
-      case match[2]
-      when 'prj'
-        project = Project.find_by_id(match[3].base62_decode)
-        next unless project
-        if project.archived?
-          "<span class='sa-type'>" \
-          "#{sanitize_input(match[2])}</span>" \
-          "#{link_to project.name,
-                     projects_archive_path} #{I18n.t('atwho.res.archived')}"
-        else
-          "<span class='sa-type'>" \
-          "#{sanitize_input(match[2])}</span>" \
-          "#{link_to project.name,
-                     project_path(project)}"
-        end
-      when 'exp'
-        experiment = Experiment.find_by_id(match[3].base62_decode)
-        next unless experiment
-        if experiment.archived?
-          "<span class='sa-type'>" \
-          "#{sanitize_input(match[2])}</span>" \
-          "#{link_to experiment.name,
-                     experiment_archive_project_path(experiment.project)} " \
-          "#{I18n.t('atwho.res.archived')}"
-        else
-          "<span class='sa-type'>"\
-          "#{sanitize_input(match[2])}</span>" \
-          "#{link_to experiment.name,
-                     canvas_experiment_path(experiment)}"
-        end
-      when 'tsk'
-        my_module = MyModule.find_by_id(match[3].base62_decode)
-        next unless my_module
-        if my_module.archived?
-          "<span class='sa-type'>" \
-          "#{sanitize_input(match[2])}</span>" \
-          "#{link_to my_module.name,
-                     module_archive_experiment_path(my_module.experiment)} " \
-          "#{I18n.t('atwho.res.archived')}"
-        else
-          "<span class='sa-type'>" \
-          "#{sanitize_input(match[2])}</span>" \
-          "#{link_to my_module.name,
-                     protocols_my_module_path(my_module)}"
-        end
-      when 'sam'
-        sample = Sample.find_by_id(match[3].base62_decode)
-        if sample
-          "<span class='glyphicon glyphicon-tint'></span>" \
-          "#{link_to(sample.name,
-                     sample_path(sample.id),
-                     class: 'sample-info-link')}"
-        else
-          "<span class='glyphicon glyphicon-tint'></span>" \
-          "#{match[1]} #{I18n.t('atwho.res.deleted')}"
-        end
-      end
-    end
-    new_text
+    SmartAnnotations::TagToHtml.new(current_user, text).html
   end
 
   # Check if text have smart annotations of users
diff --git a/app/permissions/project.rb b/app/permissions/project.rb
index 3b07cf6cd..e3701db6d 100644
--- a/app/permissions/project.rb
+++ b/app/permissions/project.rb
@@ -16,7 +16,6 @@ Canaid::Permissions.register_for(Project) do
   # project: read, read activities, read comments, read users, read archive,
   #          read notifications
   # reports: read
-  # samples: read
   can :read_project do |user, project|
     user.is_member_of_project?(project) ||
       user.is_admin_of_team?(project.team) ||
diff --git a/app/services/smart_annotations/permision_eval.rb b/app/services/smart_annotations/permision_eval.rb
new file mode 100644
index 000000000..87a14c443
--- /dev/null
+++ b/app/services/smart_annotations/permision_eval.rb
@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+module SmartAnnotations
+  class PermissionEval
+    class << self
+      include Canaid::Helpers::PermissionsHelper
+
+      def check(user, type, object)
+        send("validate_#{type}_permissions", user, object)
+      end
+
+      private
+
+      def validate_prj_permissions(user, object)
+        can_read_project?(user, object)
+      end
+
+      def validate_exp_permissions(user, object)
+        can_read_experiment?(user, object)
+      end
+
+      def validate_tsk_permissions(user, object)
+        can_read_experiment?(user, object.experiment)
+      end
+
+      def validate_sam_permissions(user, object)
+        can_read_team?(user, object.team)
+      end
+
+      def validate_rep_item_permissions(user, object)
+        can_read_team?(user, object.repository.team)
+      end
+    end
+  end
+end
diff --git a/app/services/smart_annotations/preview.rb b/app/services/smart_annotations/preview.rb
new file mode 100644
index 000000000..e6be1a24b
--- /dev/null
+++ b/app/services/smart_annotations/preview.rb
@@ -0,0 +1,77 @@
+# frozen_string_literal: true
+
+module SmartAnnotations
+  class Preview
+    class << self
+      def html(name, type, object)
+        send("generate_#{type}_snippet", name, object)
+      end
+
+      private
+
+      ROUTES = Rails.application.routes.url_helpers
+
+      def generate_prj_snippet(_, object)
+        if object.archived?
+          return "<span class='sa-type'>PRJ</span><a href='" \
+                 "#{ROUTES.projects_archive_path}'>#{object.name}</a>" \
+                 "#{I18n.t('atwho.res.archived')}"
+        end
+        "<span class='sa-type'>PRJ</span>" \
+        "<a href='#{ROUTES.project_path(object)}'>#{object.name}</a>"
+      end
+
+      def generate_exp_snippet(_, object)
+        if object.archived?
+          return "<span class='sa-type'>EXP</span>" \
+          "<a href='#{ROUTES.experiment_archive_project_path(
+                               object.project
+                             )}'>#{object.name}</a>" \
+                 "#{I18n.t('atwho.res.archived')}"
+        end
+        "<span class='sa-type'>EXP</span>" \
+        "<a href='#{ROUTES.canvas_experiment_path(object)}'>#{object.name}</a>"
+      end
+
+      def generate_tsk_snippet(_, object)
+        if object.archived?
+          return "<span class='sa-type'>TSK</span>" \
+          "<a href='#{ROUTES.module_archive_experiment_path(
+                              object.experiment
+                            )}'>#{object.name}</a>" \
+                 "#{I18n.t('atwho.res.archived')}"
+        end
+        "<span class='sa-type'>TSK</span>" \
+        "<a href='#{ROUTES.protocols_my_module_path(object)}'>" \
+        "#{object.name}</a>"
+      end
+
+      def generate_sam_snippet(name, object)
+        if object
+          return "<span class='glyphicon glyphicon-tint'></span>" \
+                  "<a href='#{ROUTES.sample_path(object.id)}' " \
+                  "class='sample-info-link'>#{object.name}</a>"
+        end
+        "<span class='glyphicon glyphicon-tint'></span>" \
+        "#{name} #{I18n.t('atwho.res.deleted')}"
+      end
+
+      def generate_rep_item_snippet(name, object)
+        if object
+          repository_name = object.repository.name
+          return "<span class='sa-type'>" \
+                 "#{trim_repository_name(repository_name)}</span>" \
+                 "<a href='#{ROUTES.repository_row_path(object)}' " \
+                 "class='record-info-link'>" \
+                 "#{object.name}</a>"
+        end
+        "<span class='sa-type'>REP</span>" \
+        "#{name} #{I18n.t('atwho.res.deleted')}"
+      end
+
+      def trim_repository_name(name)
+        name.strip.slice(0..2).upcase
+      end
+    end
+  end
+end
diff --git a/app/services/smart_annotations/tag_to_html.rb b/app/services/smart_annotations/tag_to_html.rb
new file mode 100644
index 000000000..522271404
--- /dev/null
+++ b/app/services/smart_annotations/tag_to_html.rb
@@ -0,0 +1,66 @@
+# frozen_string_literal: true
+require 'smart_annotations/permision_eval'
+require 'smart_annotations/preview'
+
+module SmartAnnotations
+  class TagToHtml
+    attr_reader :html
+
+    def initialize(user, text)
+      parse(user, text)
+    end
+
+    private
+
+    REGEX = /\[\#(.*?)~(prj|exp|tsk|sam|rep_item)~([0-9a-zA-Z]+)\]/
+    OBJECT_MAPPINGS = { prj: Project,
+                        exp: Experiment,
+                        tsk: MyModule,
+                        sam: Sample,
+                        rep_item: RepositoryRow }.freeze
+
+    def parse(user, text)
+      @html = text.gsub(REGEX) do |el|
+        value = extract_values(el)
+        type = value[:object_type]
+        begin
+          object = fetch_object(type, value[:object_id])
+          # handle samples/repository_items edge case
+          if type.in? %w(sam rep_item)
+            sample_or_repository_item(value[:name], user, type, object)
+          else
+            next unless object && SmartAnnotations::PermissionEval.check(user,
+                                                                         type,
+                                                                         object)
+            SmartAnnotations::Preview.html(nil, type, object)
+          end
+        rescue ActiveRecord::RecordNotFound
+          next
+        end
+      end
+    end
+
+    def sample_or_repository_item(name, user, type, object)
+      if object && SmartAnnotations::PermissionEval.check(user, type, object)
+        return SmartAnnotations::Preview.html(nil, type, object)
+      end
+      SmartAnnotations::Preview.html(name, type, object)
+    end
+
+    def extract_values(element)
+      match = element.match(REGEX)
+      {
+        name: match[1],
+        object_type: match[2],
+        object_id: match[3].base62_decode
+      }
+    end
+
+    def fetch_object(type, id)
+      klass = OBJECT_MAPPINGS.fetch(type.to_sym) do
+        raise ActiveRecord::RecordNotFound.new("#{type} does not exist")
+      end
+      klass.find_by_id(id)
+    end
+  end
+end
diff --git a/spec/services/smart_annotations/permission_eval_spec.rb b/spec/services/smart_annotations/permission_eval_spec.rb
new file mode 100644
index 000000000..0add140ba
--- /dev/null
+++ b/spec/services/smart_annotations/permission_eval_spec.rb
@@ -0,0 +1,47 @@
+require 'rails_helper'
+require 'smart_annotations/permision_eval'
+
+describe SmartAnnotations::PermissionEval do
+  let(:subject) { described_class }
+  let(:user) { create :user }
+  let(:team) { create :team }
+  let(:user_team) { create :user_team, user: user, team: team, role: 2 }
+  let(:project) { create :project, name: 'my project' }
+  let(:experiment) do
+    create :experiment, name: 'my experiment',
+                        project: project,
+                        created_by: user,
+                        last_modified_by: user
+  end
+  let(:task) { create :my_module, name: 'task', experiment: experiment }
+  let(:repository) { create :repository, team: team, created_by: user }
+  let(:repository_item) { create :repository_row, repository: repository }
+
+  describe '#validate_prj_permissions/2' do
+    it 'returns a boolean' do
+      value = subject.send(:validate_prj_permissions, user, project)
+      expect(value).to be_in([true, false])
+    end
+  end
+
+  describe '#validate_exp_permissions/2' do
+    it 'returns a boolean' do
+      value = subject.send(:validate_exp_permissions, user, experiment)
+      expect(value).to be_in([true, false])
+    end
+  end
+
+  describe '#validate_tsk_permissions/2' do
+    it 'returns a boolean' do
+      value = subject.send(:validate_tsk_permissions, user, task)
+      expect(value).to be_in([true, false])
+    end
+  end
+
+  describe '#validate_rep_item_permissions/2' do
+    it 'returns a boolean' do
+      value = subject.send(:validate_rep_item_permissions, user, repository_item)
+      expect(value).to be_in([true, false])
+    end
+  end
+end
diff --git a/spec/services/smart_annotations/preview_spec.rb b/spec/services/smart_annotations/preview_spec.rb
new file mode 100644
index 000000000..8ce623cd5
--- /dev/null
+++ b/spec/services/smart_annotations/preview_spec.rb
@@ -0,0 +1,63 @@
+require 'rails_helper'
+require 'smart_annotations/preview'
+
+describe SmartAnnotations::Preview do
+  let(:subject) { described_class }
+  let(:user) { create :user }
+  let(:project) { create :project, name: 'my project' }
+  let(:experiment) do
+    create :experiment, name: 'my experiment',
+                        project: project,
+                        created_by: user,
+                        last_modified_by: user
+  end
+  let(:task) { create :my_module, name: 'task', experiment: experiment }
+
+  describe 'Project annotations with type prj' do
+    it 'returns a html snippet' do
+      snippet = subject.html(nil, 'prj', project)
+      expect(snippet).to eq(
+        "<span class='sa-type'>PRJ</span>" \
+        "<a href='/projects/#{project.id}'>my project</a>"
+      )
+    end
+  end
+
+  context 'Experiment annotations with type exp' do
+    it 'returns a html snippet' do
+      snippet = subject.html(nil, 'exp', experiment)
+      expect(snippet).to eq(
+        "<span class='sa-type'>EXP</span>" \
+        "<a href='/experiments/#{experiment.id}/canvas'>my experiment</a>"
+      )
+    end
+  end
+
+  context 'MyModule annotations with type tsk' do
+    it 'returns a html snippet' do
+      snippet = subject.html(nil, 'tsk', task)
+      expect(snippet).to eq(
+        "<span class='sa-type'>TSK</span>" \
+        "<a href='/modules/#{task.id}/protocols'>task</a>"
+      )
+    end
+  end
+
+  context 'Repository item annotations with type rep_item' do
+    it 'returns a html snippet' do
+      snippet = subject.html('my item', 'rep_item', nil)
+      expect(snippet).to eq(
+        '<span class=\'sa-type\'>REP</span>my item (deleted)'
+      )
+    end
+  end
+
+  describe '#trim_repository_name/1' do
+    it 'is returns a 3 letter upcase string' do
+      trimmed_repository_name = subject.__send__(
+        :trim_repository_name, 'banana'
+      )
+      expect(trimmed_repository_name).to eq('BAN')
+    end
+  end
+end
diff --git a/spec/services/smart_annotations/tag_to_html_spec.rb b/spec/services/smart_annotations/tag_to_html_spec.rb
new file mode 100644
index 000000000..a15f3f25e
--- /dev/null
+++ b/spec/services/smart_annotations/tag_to_html_spec.rb
@@ -0,0 +1,44 @@
+require 'rails_helper'
+
+describe SmartAnnotations::TagToHtml do
+  let!(:user) { create :user }
+  let!(:team) { create :team }
+  let!(:user_team) { create :user_team, user: user, team: team, role: 2 }
+  let!(:project) { create :project, name: 'my project', team: team }
+  let!(:user_project) do
+    create :user_project, project: project, user: user, role: 0
+  end
+  let(:text) do
+    "My annotation of [#my project~prj~#{project.id.base62_encode}]"
+  end
+  let(:subject) { described_class.new(user, text) }
+  describe 'Parsed text' do
+    it 'returns a existing string with smart annotation' do
+      expect(subject.html).to eq(
+        "My annotation of <span class='sa-type'>PRJ</span>"\
+        "<a href='/projects/#{project.id}'>my project</a>"
+      )
+    end
+  end
+
+  describe '#extract_values/1' do
+    it 'returns a parsed hash of smart annotation' do
+      values = subject.send(:extract_values, '[#my project~prj~1]')
+      expect(values[:name]).to eq 'my project'
+      expect(values[:object_id]).to eq 1
+      expect(values[:object_type]).to eq 'prj'
+    end
+  end
+
+  describe '#fetch_object/2' do
+    it 'rises an error if type is not valid' do
+      expect {
+        subject.send(:fetch_object, 'banana', project.id)
+      }.to raise_error(ActiveRecord::RecordNotFound)
+    end
+
+    it 'returns the required object' do
+      expect(subject.send(:fetch_object, 'prj', project.id)).to eq project
+    end
+  end
+end

From 01a548e8b3a0b9176776a1ea17ec228689dd3a97 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Thu, 29 Mar 2018 16:11:21 +0200
Subject: [PATCH 09/23] fix hound

---
 app/services/smart_annotations/preview.rb     | 20 ++++++++-----------
 app/services/smart_annotations/tag_to_html.rb |  1 +
 2 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/app/services/smart_annotations/preview.rb b/app/services/smart_annotations/preview.rb
index e6be1a24b..108e4af52 100644
--- a/app/services/smart_annotations/preview.rb
+++ b/app/services/smart_annotations/preview.rb
@@ -23,11 +23,9 @@ module SmartAnnotations
 
       def generate_exp_snippet(_, object)
         if object.archived?
-          return "<span class='sa-type'>EXP</span>" \
-          "<a href='#{ROUTES.experiment_archive_project_path(
-                               object.project
-                             )}'>#{object.name}</a>" \
-                 "#{I18n.t('atwho.res.archived')}"
+          return "<span class='sa-type'>EXP</span><a href='" \
+                 "#{ROUTES.experiment_archive_project_path(object.project)}'>" \
+                 "#{object.name}</a> #{I18n.t('atwho.res.archived')}"
         end
         "<span class='sa-type'>EXP</span>" \
         "<a href='#{ROUTES.canvas_experiment_path(object)}'>#{object.name}</a>"
@@ -35,11 +33,10 @@ module SmartAnnotations
 
       def generate_tsk_snippet(_, object)
         if object.archived?
-          return "<span class='sa-type'>TSK</span>" \
-          "<a href='#{ROUTES.module_archive_experiment_path(
-                              object.experiment
-                            )}'>#{object.name}</a>" \
-                 "#{I18n.t('atwho.res.archived')}"
+          return "<span class='sa-type'>TSK</span><a href='" \
+                 "#{ROUTES.module_archive_experiment_path(
+                   object.experiment
+                 )}'>#{object.name}</a> #{I18n.t('atwho.res.archived')}"
         end
         "<span class='sa-type'>TSK</span>" \
         "<a href='#{ROUTES.protocols_my_module_path(object)}'>" \
@@ -62,8 +59,7 @@ module SmartAnnotations
           return "<span class='sa-type'>" \
                  "#{trim_repository_name(repository_name)}</span>" \
                  "<a href='#{ROUTES.repository_row_path(object)}' " \
-                 "class='record-info-link'>" \
-                 "#{object.name}</a>"
+                 "class='record-info-link'>#{object.name}</a>"
         end
         "<span class='sa-type'>REP</span>" \
         "#{name} #{I18n.t('atwho.res.deleted')}"
diff --git a/app/services/smart_annotations/tag_to_html.rb b/app/services/smart_annotations/tag_to_html.rb
index 522271404..69616a6f8 100644
--- a/app/services/smart_annotations/tag_to_html.rb
+++ b/app/services/smart_annotations/tag_to_html.rb
@@ -1,4 +1,5 @@
 # frozen_string_literal: true
+
 require 'smart_annotations/permision_eval'
 require 'smart_annotations/preview'
 

From 802e917e69dfb22202ce507a99c94cde83e5cc01 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Fri, 30 Mar 2018 09:47:27 +0200
Subject: [PATCH 10/23] updated repository import modal html [fixes SCI-2235]

---
 app/views/repositories/_parse_records_modal.html.erb | 8 +++++++-
 config/locales/en.yml                                | 2 ++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/app/views/repositories/_parse_records_modal.html.erb b/app/views/repositories/_parse_records_modal.html.erb
index 693b12650..44c398a16 100644
--- a/app/views/repositories/_parse_records_modal.html.erb
+++ b/app/views/repositories/_parse_records_modal.html.erb
@@ -13,7 +13,7 @@
                              remote: true) do |f|%>
       <%= f.hidden_field :team_id, value: current_team.id %>
       <div class="modal-body">
-        <h4><%= t("teams.parse_sheet.help_text") %></h4>
+        <p><%= t("teams.parse_sheet.help_text") %></p>
         <div style="overflow-x: scroll">
           <table class="table parse-records-table" style="display: block">
             <thead>
@@ -62,6 +62,12 @@
 
         <div id="import-errors-container">
         </div>
+        <div class="alert alert-info" role="alert">
+          <ul>
+            <li><%= t('repositories.modal_parse.warning_1') %></li>
+            <li><%= t('repositories.modal_parse.warning_2') %></li>
+          </ul>
+        </div>
       </div>
       <div class="modal-footer">
         <button type="button" class="btn btn-default" data-dismiss="modal" onClick="pageReload()"><%= t('general.cancel')%></button>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index f15a06373..384afc2c7 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -962,6 +962,8 @@ en:
       delete: "Delete column"
     modal_parse:
       title: 'Import items'
+      warning_1: 'Be careful when importing into Dropdown column/s! Each new unique cell value from the file will create a new Dropdown option. This could result in large amounts of Dropdown options.'
+      warning_2: 'Importing into file columns is not supported.'
     modal_import:
       title: 'Import items'
       notice: 'You may upload .csv file (comma separated) or tab separated file (.txt or .tsv) or Excel file (.xlsx). First row should include header names, followed by rows with sample data.'

From 10b5e1de84b7c4e510314dd921819e83dcb44e11 Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Fri, 30 Mar 2018 09:54:57 +0200
Subject: [PATCH 11/23] refactor typography

---
 app/assets/stylesheets/constants.scss         | 48 ++++++++++---------
 app/assets/stylesheets/notifications.scss     |  6 +--
 app/assets/stylesheets/partials/_sidebar.scss |  2 +-
 app/assets/stylesheets/projects.scss          |  8 ++--
 app/assets/stylesheets/reports.scss           |  2 +-
 app/assets/stylesheets/search.scss            |  2 +-
 .../stylesheets/themes/main_navigation.scss   | 12 ++---
 app/assets/stylesheets/themes/menu_bar.scss   |  2 +-
 app/assets/stylesheets/themes/scinote.scss    | 26 ++--------
 9 files changed, 46 insertions(+), 62 deletions(-)

diff --git a/app/assets/stylesheets/constants.scss b/app/assets/stylesheets/constants.scss
index 8404a75b0..35d308d18 100644
--- a/app/assets/stylesheets/constants.scss
+++ b/app/assets/stylesheets/constants.scss
@@ -1,3 +1,5 @@
+@import url(https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic&subset=latin,latin-ext);
+
 //==============================================================================
 // Colors
 //==============================================================================
@@ -49,33 +51,33 @@ $gray-light: $color-dove-gray;
 $gray-lighter: $color-concrete;
 
 // Scaffolding
-$body-bg: $color-white;
-$text-color: $gray-dark;
+$body-bg: $color-concrete;
+$text-color: $color-emperor;
 $link-color: $brand-primary;
 $link-hover-color: darken($link-color, 15%);
 $link-hover-decoration: underline;
 
-// // Typography
-// $font-family-sans-serif: "Open Sans", Arial, Helvetica, sans-serif;
-// $font-family-serif: Georgia, "Times New Roman", Times, serif;
-// $font-family-monospace: Menlo, Monaco, Consolas, "Courier New", monospace;
-// $font-family-base: $font-family-sans-serif;
-// $font-size-base: 14px;
-// $font-size-large: ceil(($font-size-base * 1.25));
-// $font-size-small: ceil(($font-size-base * 0.85));
-// $font-size-h1: floor(($font-size-base * 2.6));
-// $font-size-h2: floor(($font-size-base * 2.15));
-// $font-size-h3: ceil(($font-size-base * 1.7));
-// $font-size-h4: ceil(($font-size-base * 1.25));
-// $font-size-h5: $font-size-base;
-// $font-size-h6: ceil(($font-size-base * 0.85));
-// $line-height-base: 1.428571429;
-// $line-height-computed: floor(($font-size-base * $line-height-base));
-// $headings-font-family: inherit;
-// $headings-font-weight: 500;
-// $headings-line-height: 1.1;
-// $headings-color: inherit;
-//
+// Typography
+$font-family-sans-serif: "Open Sans", Arial, Helvetica, sans-serif;
+$font-family-serif: Georgia, "Times New Roman", Times, serif;
+$font-family-monospace: Menlo, Monaco, Consolas, "Courier New", monospace;
+$font-family-base: $font-family-sans-serif;
+$font-size-base: 14px;
+$font-size-large: ceil(($font-size-base * 1.1)); //16px
+$font-size-small: ceil(($font-size-base * .9)); //13px
+$font-size-h1: floor(($font-size-base * 2.6)); //36px
+$font-size-h2: floor(($font-size-base * 2.15)); //30px
+$font-size-h3: ceil(($font-size-base * 1.7)); //24px
+$font-size-h4: ceil(($font-size-base * 1.25)); //18px
+$font-size-h5: $font-size-base; //14px
+$font-size-h6: ceil(($font-size-base * .85)); //12px
+$line-height-base: 1.428571429;
+$line-height-computed: floor(($font-size-base * $line-height-base));
+$headings-font-family: inherit;
+$headings-font-weight: 500;
+$headings-line-height: 1.1;
+$headings-color: inherit;
+
 // // Iconography
 // $icon-font-path: "../fonts/";
 // $icon-font-name: "glyphicons-halflings-regular";
diff --git a/app/assets/stylesheets/notifications.scss b/app/assets/stylesheets/notifications.scss
index 68e27dbf9..e2b79df7e 100644
--- a/app/assets/stylesheets/notifications.scss
+++ b/app/assets/stylesheets/notifications.scss
@@ -53,7 +53,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: inline-block;
-    font-size: 13px;
+    font-size: $font-size-small;
     height: 30px;
     padding-top: 5px;
     width: 30px;
@@ -64,7 +64,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: inline-block;
-    font-size: 13px;
+    font-size: $font-size-small;
     height: 30px;
     padding-top: 5px;
     width: 30px;
@@ -75,7 +75,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: inline-block;
-    font-size: 13px;
+    font-size: $font-size-small;
     height: 30px;
     padding-top: 5px;
     width: 30px;
diff --git a/app/assets/stylesheets/partials/_sidebar.scss b/app/assets/stylesheets/partials/_sidebar.scss
index 1ecba2cb7..ec830b72e 100644
--- a/app/assets/stylesheets/partials/_sidebar.scss
+++ b/app/assets/stylesheets/partials/_sidebar.scss
@@ -63,7 +63,7 @@ $toggle-btn-size: 50px;
         width: $toggle-btn-size;
         margin-left: ($wrapper-width - $toggle-btn-size);
         margin-top: -$toggle-btn-size;
-        font-size: 20pt;
+        font-size: $font-size-h3;
         background: $brand-primary;
         border-left: 2px solid darken($brand-primary, 10%);
         border-bottom: 2px solid darken($brand-primary, 10%);
diff --git a/app/assets/stylesheets/projects.scss b/app/assets/stylesheets/projects.scss
index 7477d6001..1ebbb2ef0 100644
--- a/app/assets/stylesheets/projects.scss
+++ b/app/assets/stylesheets/projects.scss
@@ -326,7 +326,7 @@ path, ._jsPlumb_endpoint {
 
   span {
     font-weight: bold;
-    font-size: 16px;
+    font-size: $font-size-large;
     text-transform: uppercase;
     display: block;
     margin-top: 20%;
@@ -400,7 +400,7 @@ li.module-hover {
           margin-top: 5px;
           font-family: 'Glyphicons Halflings';
           color: $color-white;
-          font-size: 12pt;
+          font-size: $font-size-large;
 
           &:before {
             content: "\e221";
@@ -412,7 +412,7 @@ li.module-hover {
 
     .glyphicon {
       color: $color-white;
-      font-size: 12pt;
+      font-size: $font-size-h6;
     }
 
     a.btn-link {
@@ -463,7 +463,7 @@ li.module-hover {
   .experiment-no-description {
     color: $color-alto;
     display: block;
-    font-size: 18px;
+    font-size: $font-size-h4;
     font-weight: bold;
     text-align: center;
 
diff --git a/app/assets/stylesheets/reports.scss b/app/assets/stylesheets/reports.scss
index 4027665be..180cb7c48 100644
--- a/app/assets/stylesheets/reports.scss
+++ b/app/assets/stylesheets/reports.scss
@@ -223,7 +223,7 @@ label {
     }
     .controls {
       margin-right: 15px;
-      font-size: 12pt;
+      font-size: $font-size-h6;
       opacity: 0.05;
     }
   }
diff --git a/app/assets/stylesheets/search.scss b/app/assets/stylesheets/search.scss
index 932e1cce1..3b7a86526 100644
--- a/app/assets/stylesheets/search.scss
+++ b/app/assets/stylesheets/search.scss
@@ -9,5 +9,5 @@
   padding-top: 20px;
 }
 .search-asset-text-data{
-  font-size: 14px;
+  font-size: $font-size-base;
 }
diff --git a/app/assets/stylesheets/themes/main_navigation.scss b/app/assets/stylesheets/themes/main_navigation.scss
index a5f177bd1..e4a25938b 100644
--- a/app/assets/stylesheets/themes/main_navigation.scss
+++ b/app/assets/stylesheets/themes/main_navigation.scss
@@ -7,7 +7,7 @@
 
 #notifications-dropdown {
   .fa-bell {
-    font-size: 15px;
+    font-size: $font-size-large;
     position: absolute;
   }
 
@@ -88,7 +88,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: block;
-    font-size: 23px;
+    font-size: $font-size-h3;
     height: 45px;
     padding-top: 5px;
     width: 45px;
@@ -99,7 +99,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: block;
-    font-size: 23px;
+    font-size: $font-size-h3;
     height: 45px;
     padding-top: 5px;
     width: 45px;
@@ -110,7 +110,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: block;
-    font-size: 23px;
+    font-size: $font-size-h3;
     height: 45px;
     padding-top: 8px;
     width: 45px;
@@ -222,7 +222,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: block !important;
-    font-size: 15px;
+    font-size: $font-size-base;
     height: 30px;
     margin-right: 15px;
     padding: 7px;
@@ -236,7 +236,7 @@
     border-radius: 50%;
     color: $color-concrete;
     display: block !important;
-    font-size: 15px;
+    font-size: $font-size-base;
     height: 30px;
     margin-right: 15px;
     padding: 8px;
diff --git a/app/assets/stylesheets/themes/menu_bar.scss b/app/assets/stylesheets/themes/menu_bar.scss
index 7e2a9d012..0c492a990 100644
--- a/app/assets/stylesheets/themes/menu_bar.scss
+++ b/app/assets/stylesheets/themes/menu_bar.scss
@@ -18,7 +18,7 @@
     & > a {
       color: $color-silver-chalice;
       display: grid;
-      font-size: 12px;
+      font-size: $font-size-h6;
       margin-left: auto;
       margin-right: auto;
       padding: 10px;
diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss
index 00245ed39..58bbf1831 100644
--- a/app/assets/stylesheets/themes/scinote.scss
+++ b/app/assets/stylesheets/themes/scinote.scss
@@ -73,7 +73,7 @@ table {
 }
 
 .blockquote-search {
-  font-size: 14px;
+  font-size: $font-size-base;
   margin-bottom: 10px;
 }
 
@@ -89,18 +89,8 @@ table {
 
 /** Skin **/
 
-
-@import url(https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic&subset=latin,latin-ext);
-
 body {
-  background-color: $color-concrete;
-  color: $color-emperor;
-  font-family: "Open Sans",Arial,Helvetica,sans-serif;
-  font-size: 13px;
-}
-
-a {
-  color: $brand-primary;
+  font-size: $font-size-small;
 }
 
 .jumbotron {
@@ -343,7 +333,7 @@ a[data-toggle="tooltip"] {
   padding: 13px;
 
   .glyphicon.glyphicon-info-sign {
-    font-size: 16px;
+    font-size: $font-size-large;
     margin-top: 4px;
   }
 }
@@ -711,14 +701,6 @@ ul.content-activities {
       text-align: justify;
     }
   }
-  li.activity-date-item {
-    font-size: 1.4em;
-
-    & > span {
-      padding-left: 2em;
-      padding-right: 2em;
-    }
-  }
 }
 
 ul.content-module-activities {
@@ -1290,7 +1272,7 @@ table.dataTable {
 // Image preview modal
 .modal-image-preview {
   background: transparent;
-  font-size: 16px;
+  font-size: $font-size-large;
   padding-right: 0 !important;
   z-index: 1060;
 

From cc855cda86dcc8c1446ad9c5286c17654aa8cc04 Mon Sep 17 00:00:00 2001
From: Oleksii Kriuchykhin <okriuchykhin@biosistemika.com>
Date: Fri, 30 Mar 2018 12:48:34 +0200
Subject: [PATCH 12/23] Fix translations [SCI-2205]

---
 app/views/repositories/_repository_row_info_modal.html.erb | 2 +-
 config/locales/en.yml                                      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/views/repositories/_repository_row_info_modal.html.erb b/app/views/repositories/_repository_row_info_modal.html.erb
index b107e9786..7f321e2c4 100644
--- a/app/views/repositories/_repository_row_info_modal.html.erb
+++ b/app/views/repositories/_repository_row_info_modal.html.erb
@@ -9,7 +9,7 @@
       <div class="modal-body">
         <ol class="breadcrumb breadcrumb-repository">
           <span class="fa fa-cubes" aria-hidden="true"></span>
-          <%= "#{t('repositories.repository')}: #{@repository_row.repository.name}" %>
+          <%= t('repositories.repository', name: @repository_row.repository.name) %>
         </ol>
         <p>
           <span>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 3f61578f2..fe79f90a7 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -873,7 +873,7 @@ en:
       success_flash: "Table result successfully deleted."
 
   repositories:
-    repository: "Repository"
+    repository: "Repository: %{name}"
     index:
       head_title: "Repositories"
       title: "Repositories"

From 69b83a3f3d8db77dbbd51a0c904cc63e454992e2 Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Fri, 30 Mar 2018 12:50:06 +0200
Subject: [PATCH 13/23] fix travis

---
 features/step_definitions/users_steps.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/features/step_definitions/users_steps.rb b/features/step_definitions/users_steps.rb
index 1a575e9b9..c3e9a92ee 100644
--- a/features/step_definitions/users_steps.rb
+++ b/features/step_definitions/users_steps.rb
@@ -19,8 +19,8 @@ end
 
 Given(/^"([^"]*)" is signed in with "([^"]*)"$/) do |email, password|
   visit '/users/sign_in'
-  fill_in 'user_email', with: email
-  fill_in 'user_password', with: password
+  fill_in '#user_email', with: email
+  fill_in '#user_password', with: password
   click_button 'Log in'
   @current_user = User.find_by_email(email)
 end
@@ -35,7 +35,7 @@ end
 
 Given("I click on Reset Password link in the reset password email for user {string}") do |email|
   visit new_user_password_path
-  fill_in 'user_email', with: email
+  fill_in '#user_email', with: email
   click_button 'Send me reset password instruction'
   Delayed::Worker.new.work_off
   sleep 10
@@ -52,6 +52,6 @@ Given(/^I am on Log in page$/) do
 end
 
 Then(/^I fill in Email "([^"]*)" and Password "([^"]*)"$/) do |email, password|
-  fill_in 'user_email', with: email
-  fill_in 'user_password', with: password
+  fill_in '#user_email', with: email
+  fill_in '#user_password', with: password
 end

From 5f0d33d75e5f2e1c8070afe7eb731d13c65900ab Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Fri, 30 Mar 2018 16:47:23 +0200
Subject: [PATCH 14/23] fix travis again

---
 app/assets/stylesheets/constants.scss    |  2 +-
 features/step_definitions/users_steps.rb | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/app/assets/stylesheets/constants.scss b/app/assets/stylesheets/constants.scss
index 35d308d18..777b7f43d 100644
--- a/app/assets/stylesheets/constants.scss
+++ b/app/assets/stylesheets/constants.scss
@@ -1,4 +1,4 @@
-@import url(https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic&subset=latin,latin-ext);
+// @import url(https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic&subset=latin,latin-ext);
 
 //==============================================================================
 // Colors
diff --git a/features/step_definitions/users_steps.rb b/features/step_definitions/users_steps.rb
index c3e9a92ee..1a575e9b9 100644
--- a/features/step_definitions/users_steps.rb
+++ b/features/step_definitions/users_steps.rb
@@ -19,8 +19,8 @@ end
 
 Given(/^"([^"]*)" is signed in with "([^"]*)"$/) do |email, password|
   visit '/users/sign_in'
-  fill_in '#user_email', with: email
-  fill_in '#user_password', with: password
+  fill_in 'user_email', with: email
+  fill_in 'user_password', with: password
   click_button 'Log in'
   @current_user = User.find_by_email(email)
 end
@@ -35,7 +35,7 @@ end
 
 Given("I click on Reset Password link in the reset password email for user {string}") do |email|
   visit new_user_password_path
-  fill_in '#user_email', with: email
+  fill_in 'user_email', with: email
   click_button 'Send me reset password instruction'
   Delayed::Worker.new.work_off
   sleep 10
@@ -52,6 +52,6 @@ Given(/^I am on Log in page$/) do
 end
 
 Then(/^I fill in Email "([^"]*)" and Password "([^"]*)"$/) do |email, password|
-  fill_in '#user_email', with: email
-  fill_in '#user_password', with: password
+  fill_in 'user_email', with: email
+  fill_in 'user_password', with: password
 end

From 6a20c37449bab02a26e4bf878babfb61a76b3626 Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Fri, 30 Mar 2018 17:16:18 +0200
Subject: [PATCH 15/23] fix travis againnnnn

---
 app/assets/javascripts/projects/index.js.erb | 4 ++--
 app/assets/stylesheets/constants.scss        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/assets/javascripts/projects/index.js.erb b/app/assets/javascripts/projects/index.js.erb
index eeb9515d9..f30806a7e 100644
--- a/app/assets/javascripts/projects/index.js.erb
+++ b/app/assets/javascripts/projects/index.js.erb
@@ -452,12 +452,12 @@
       .find('.form-submit-link')
       .css({
         'pointer-events': 'auto',
-        'color': '<%= Constants::COLOR_NERO %>'});
+        'color': '<%= Constants::COLOR_BLACK %>'});
       $(el)
       .find("[data-action='edit']")
       .css({
         'pointer-events': 'auto',
-        'color': '<%= Constants::COLOR_NERO %>'});
+        'color': '<%= Constants::COLOR_BLACK %>'});
     });
   }
 
diff --git a/app/assets/stylesheets/constants.scss b/app/assets/stylesheets/constants.scss
index 777b7f43d..35d308d18 100644
--- a/app/assets/stylesheets/constants.scss
+++ b/app/assets/stylesheets/constants.scss
@@ -1,4 +1,4 @@
-// @import url(https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic&subset=latin,latin-ext);
+@import url(https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic&subset=latin,latin-ext);
 
 //==============================================================================
 // Colors

From 7dfec94ffce48c4a6a307d882b88b4437d5db210 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Tue, 3 Apr 2018 09:43:12 +0200
Subject: [PATCH 16/23] remove samples from smart annotations

---
 app/services/smart_annotations/permision_eval.rb |  4 ----
 app/services/smart_annotations/preview.rb        | 10 ----------
 app/services/smart_annotations/tag_to_html.rb    |  7 +++----
 3 files changed, 3 insertions(+), 18 deletions(-)

diff --git a/app/services/smart_annotations/permision_eval.rb b/app/services/smart_annotations/permision_eval.rb
index 87a14c443..dc8dd41ed 100644
--- a/app/services/smart_annotations/permision_eval.rb
+++ b/app/services/smart_annotations/permision_eval.rb
@@ -23,10 +23,6 @@ module SmartAnnotations
         can_read_experiment?(user, object.experiment)
       end
 
-      def validate_sam_permissions(user, object)
-        can_read_team?(user, object.team)
-      end
-
       def validate_rep_item_permissions(user, object)
         can_read_team?(user, object.repository.team)
       end
diff --git a/app/services/smart_annotations/preview.rb b/app/services/smart_annotations/preview.rb
index 108e4af52..791b3d2af 100644
--- a/app/services/smart_annotations/preview.rb
+++ b/app/services/smart_annotations/preview.rb
@@ -43,16 +43,6 @@ module SmartAnnotations
         "#{object.name}</a>"
       end
 
-      def generate_sam_snippet(name, object)
-        if object
-          return "<span class='glyphicon glyphicon-tint'></span>" \
-                  "<a href='#{ROUTES.sample_path(object.id)}' " \
-                  "class='sample-info-link'>#{object.name}</a>"
-        end
-        "<span class='glyphicon glyphicon-tint'></span>" \
-        "#{name} #{I18n.t('atwho.res.deleted')}"
-      end
-
       def generate_rep_item_snippet(name, object)
         if object
           repository_name = object.repository.name
diff --git a/app/services/smart_annotations/tag_to_html.rb b/app/services/smart_annotations/tag_to_html.rb
index 69616a6f8..cb0193a0e 100644
--- a/app/services/smart_annotations/tag_to_html.rb
+++ b/app/services/smart_annotations/tag_to_html.rb
@@ -13,11 +13,10 @@ module SmartAnnotations
 
     private
 
-    REGEX = /\[\#(.*?)~(prj|exp|tsk|sam|rep_item)~([0-9a-zA-Z]+)\]/
+    REGEX = /\[\#(.*?)~(prj|exp|tsk|rep_item)~([0-9a-zA-Z]+)\]/
     OBJECT_MAPPINGS = { prj: Project,
                         exp: Experiment,
                         tsk: MyModule,
-                        sam: Sample,
                         rep_item: RepositoryRow }.freeze
 
     def parse(user, text)
@@ -26,8 +25,8 @@ module SmartAnnotations
         type = value[:object_type]
         begin
           object = fetch_object(type, value[:object_id])
-          # handle samples/repository_items edge case
-          if type.in? %w(sam rep_item)
+          # handle repository_items edge case
+          if type == 'rep_item'
             sample_or_repository_item(value[:name], user, type, object)
           else
             next unless object && SmartAnnotations::PermissionEval.check(user,

From e5e92eb215e72133bcbc036454190a7feb96827d Mon Sep 17 00:00:00 2001
From: mlorb <mlorber@biosistemika.com>
Date: Tue, 3 Apr 2018 10:28:39 +0200
Subject: [PATCH 17/23] fix the rest of the constants

---
 .../Navigation/components/GlobalActivitiesModal.jsx    | 10 +++++-----
 app/javascript/src/components/data_grid/index.jsx      |  4 ++--
 app/javascript/src/components/data_table/index.jsx     |  4 ++--
 app/javascript/src/config/constants/colors.js          |  8 +++-----
 config/initializers/constants.rb                       |  4 ++--
 5 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/app/javascript/src/components/Navigation/components/GlobalActivitiesModal.jsx b/app/javascript/src/components/Navigation/components/GlobalActivitiesModal.jsx
index 90c834123..6a8f613c5 100644
--- a/app/javascript/src/components/Navigation/components/GlobalActivitiesModal.jsx
+++ b/app/javascript/src/components/Navigation/components/GlobalActivitiesModal.jsx
@@ -14,8 +14,8 @@ import ActivityDateElement from "./ActivityDateElement";
 import {
   WHITE_COLOR,
   COLOR_CONCRETE,
-  COLOR_MINE_SHAFT,
-  COLOR_GRAY_LIGHT_YADCF
+  COLOR_EMPEROR,
+  COLOR_ALTO
 } from "../../../config/constants/colors";
 
 const StyledBottom = styled(Button)`
@@ -37,14 +37,14 @@ const StyledBottom = styled(Button)`
   -moz-user-select: none;
   -ms-user-select: none;
   user-select: none;
-  color: ${COLOR_MINE_SHAFT};
+  color: ${COLOR_EMPEROR};
   background-color: ${WHITE_COLOR};
-  border-color: ${COLOR_GRAY_LIGHT_YADCF};
+  border-color: ${COLOR_ALTO};
 `;
 
 const StyledModalBody = styled(Modal.Body)`
   background-color: ${COLOR_CONCRETE};
-  color: ${COLOR_MINE_SHAFT};
+  color: ${COLOR_EMPEROR};
 `;
 
 type Props = {
diff --git a/app/javascript/src/components/data_grid/index.jsx b/app/javascript/src/components/data_grid/index.jsx
index a64fc315d..0c1de4b98 100644
--- a/app/javascript/src/components/data_grid/index.jsx
+++ b/app/javascript/src/components/data_grid/index.jsx
@@ -4,7 +4,7 @@ import ReactDataGrid from 'react-data-grid';
 import styled from "styled-components";
 import {
   WHITE_COLOR,
-  COLOR_GRAY
+  COLOR_SILVER_CHALICE
 } from "../../config/constants/colors";
 
 const StyledReactDataGrid = styled(ReactDataGrid)`
@@ -16,7 +16,7 @@ const StyledReactDataGrid = styled(ReactDataGrid)`
 
   .react-grid-Header {
     .react-grid-HeaderCell {
-      background-color: ${COLOR_GRAY};
+      background-color: ${COLOR_SILVER_CHALICE};
 
       color: ${WHITE_COLOR};
       font-weight: normal;
diff --git a/app/javascript/src/components/data_table/index.jsx b/app/javascript/src/components/data_table/index.jsx
index 45a4b05f5..1616aa990 100644
--- a/app/javascript/src/components/data_table/index.jsx
+++ b/app/javascript/src/components/data_table/index.jsx
@@ -5,14 +5,14 @@ import styled from "styled-components";
 import { FormattedMessage } from "react-intl";
 import {
   WHITE_COLOR,
-  COLOR_GRAY,
+  COLOR_SILVER_CHALICE,
   COLOR_ALTO,
   COLOR_ALABASTER
 } from "../../config/constants/colors";
 
 const StyledBootstrapTable = styled(BootstrapTable)`
   thead {
-    background-color: ${COLOR_GRAY};
+    background-color: ${COLOR_SILVER_CHALICE};
 
     > tr > th,
     > tr > td {
diff --git a/app/javascript/src/config/constants/colors.js b/app/javascript/src/config/constants/colors.js
index 63ea391e7..8f428f2ca 100644
--- a/app/javascript/src/config/constants/colors.js
+++ b/app/javascript/src/config/constants/colors.js
@@ -7,16 +7,14 @@ export const BORDER_LIGHT_COLOR = "#e3e3e3";
 export const WILD_SAND_COLOR = "#f5f5f5";
 export const MYSTIC_COLOR = "#eaeff2";
 export const COLOR_CONCRETE = "#f2f2f2";
-export const COLOR_MINE_SHAFT = "#333";
+export const COLOR_EMPEROR = "#333";
 export const COLOR_BLACK = "#000";
-export const COLOR_GRAY_LIGHT_YADCF = "#ccc";
+export const COLOR_ALTO = "#ccc";
 export const ICON_GREEN_COLOR = "#8fd13f";
 export const NOTIFICATION_YES = "#5a8921";
 export const NOTIFICATION_YES_BORDER = "#4d751c";
 export const SIDEBAR_HOVER_GRAY_COLOR = "#D2D2D2";
 
-export const COLOR_ALTO = "#dddddd";
-export const COLOR_GRAY = "#909088";
+export const COLOR_SILVER_CHALICE = "#909088";
 export const COLOR_ALABASTER = "#fcfcfc";
-export const COLOR_APPLE_BLOSSOM = "#a94442";
 export const COLOR_ORANGE = "#ff900b";
diff --git a/config/initializers/constants.rb b/config/initializers/constants.rb
index 5af86d880..6b0322c74 100644
--- a/config/initializers/constants.rb
+++ b/config/initializers/constants.rb
@@ -144,8 +144,8 @@ class Constants
   ].freeze
 
   # Theme colors
-  COLOR_THEME_PRIMARY = '#37a0d9'.freeze # $brand-primary
-  COLOR_THEME_SECONDARY = '#8fd13f'.freeze # $brand-default
+  BRAND_PRIMARY = '#37a0d9'.freeze # $brand-primary
+  BRAND_DEFAULT = '#8fd13f'.freeze # $brand-default
 
   # Grayscale colors
   COLOR_WHITE = '#ffffff'.freeze # $color-white

From 3d5137b56f1a7967b63fe415e6551eaf99ccf119 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Tue, 3 Apr 2018 11:22:23 +0200
Subject: [PATCH 18/23] change export model wording [fixes SCI-2239]

---
 app/views/repositories/_export_repository_modal.html.erb | 4 +++-
 config/locales/en.yml                                    | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/app/views/repositories/_export_repository_modal.html.erb b/app/views/repositories/_export_repository_modal.html.erb
index c6cd2ce0b..37207553d 100644
--- a/app/views/repositories/_export_repository_modal.html.erb
+++ b/app/views/repositories/_export_repository_modal.html.erb
@@ -12,7 +12,9 @@
            <h4 class="modal-title"><%=t 'zip_export.modal_label' %></h4>
          </div>
          <div class="modal-body">
-           <%=t('zip_export.repository_html', repository: repository.name) %>
+           <div><%=t('zip_export.repository_header_html', repository: repository.name) %></div>
+           <div class="alert alert-info" role="alert"><%=t 'zip_export.files_alert' %></div>
+           <div><%=t 'zip_export.repository_footer_html' %></div>
          </div>
          <div class="modal-footer">
            <button type='button' class='btn btn-primary' data-dismiss='modal' id='export-repositories'> <%=t 'my_modules.repository.export' %> </button>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index bfb7bfb84..7ea2f1f0b 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1845,7 +1845,9 @@ en:
     expired_description: 'Please export the data again in order to receive a new link.'
     modal_label: 'Export request received'
     modal_html: "<p>Your export request is being processed.</p><p>When completed we will <strong>send an email to %{email}</strong> inbox with a link to your exported samples. Note that the link will expire in 7 days.</p>"
-    repository_html: '<p>You are about to export selected items in repository %{repository}</p> <br> Repository will be exported in a .csv file format. You will receive <strong>email with a link</strong> where you can download it.'
+    repository_header_html: 'You are about to export selected items in inventory %{repository}'
+    files_alert: 'Files uploaded to inventory items will not be exported. Only filenames will be exported.'
+    repository_footer_html: 'Inventory will be exported in a .csv file format. You will receive <strong>email with a link</strong> where you can download it.'
     export_error: "Error when creating zip export."
 
   # This section contains general words that can be used in any parts of

From 8a156ad91e48e8a9f20c264b384913381c141ba7 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Tue, 3 Apr 2018 13:05:25 +0200
Subject: [PATCH 19/23] change method name

---
 app/services/smart_annotations/tag_to_html.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/services/smart_annotations/tag_to_html.rb b/app/services/smart_annotations/tag_to_html.rb
index cb0193a0e..0e4741b4c 100644
--- a/app/services/smart_annotations/tag_to_html.rb
+++ b/app/services/smart_annotations/tag_to_html.rb
@@ -27,7 +27,7 @@ module SmartAnnotations
           object = fetch_object(type, value[:object_id])
           # handle repository_items edge case
           if type == 'rep_item'
-            sample_or_repository_item(value[:name], user, type, object)
+            repository_item(value[:name], user, type, object)
           else
             next unless object && SmartAnnotations::PermissionEval.check(user,
                                                                          type,
@@ -40,7 +40,7 @@ module SmartAnnotations
       end
     end
 
-    def sample_or_repository_item(name, user, type, object)
+    def repository_item(name, user, type, object)
       if object && SmartAnnotations::PermissionEval.check(user, type, object)
         return SmartAnnotations::Preview.html(nil, type, object)
       end

From e630d3113f0f2ac89cc761a6db2dff8b7564fd83 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 4 Apr 2018 11:55:11 +0200
Subject: [PATCH 20/23] add ID column to repository [fixes SCI-2206]

---
 .../repositories/repository_datatable.js.erb  | 20 +++++++++++++------
 app/helpers/repository_datatable_helper.rb    |  7 ++++---
 app/models/concerns/searchable_model.rb       | 14 +++++++++++--
 app/models/my_module.rb                       |  2 ++
 app/services/repository_datatable_service.rb  |  5 ++++-
 app/services/repository_zip_export.rb         | 12 +++++++----
 .../_repository_row_info_modal.html.erb       |  9 +++++++--
 .../repositories/_repository_table.html.erb   |  3 ++-
 .../search/results/_repositories.html.erb     | 19 +++++++++++-------
 config/initializers/constants.rb              | 10 +++++-----
 config/locales/en.yml                         |  2 ++
 11 files changed, 72 insertions(+), 31 deletions(-)

diff --git a/app/assets/javascripts/repositories/repository_datatable.js.erb b/app/assets/javascripts/repositories/repository_datatable.js.erb
index 0544fa549..e3197df3c 100644
--- a/app/assets/javascripts/repositories/repository_datatable.js.erb
+++ b/app/assets/javascripts/repositories/repository_datatable.js.erb
@@ -47,7 +47,7 @@ var RepositoryDatatable = (function(global) {
     originalHeader = $(TABLE_ID + ' thead').children().clone();
     viewAssigned = 'assigned';
     TABLE = $(TABLE_ID).DataTable({
-      order: [[2, 'desc']],
+      order: [[3, 'desc']],
       dom: "R<'row'<'col-sm-9-custom toolbar'l><'col-sm-3-custom'f>>tpi",
       stateSave: true,
       processing: true,
@@ -84,7 +84,12 @@ var RepositoryDatatable = (function(global) {
         orderable: true,
         sWidth: '1%'
       }, {
-       targets: 2,
+        targets: 2,
+        searchable: true,
+        orderable: true,
+        sWidth: '1%'
+      }, {
+       targets: 3,
        render: function(data, type, row) {
          return "<a href='" + row.recordInfoUrl + "'" +
                 "class='record-info-link'>" + data + '</a>';
@@ -255,15 +260,18 @@ var RepositoryDatatable = (function(global) {
             case 'assigned':
               val = -2;
               break;
-            case 'row-name':
+            case 'row-id':
               val = -3;
-              break;
-            case 'added-by':
+              break
+            case 'row-name':
               val = -4;
               break;
-            case 'added-on':
+            case 'added-by':
               val = -5;
               break;
+            case 'added-on':
+              val = -6;
+              break;
             default:
               val = th.attr('id');
           }
diff --git a/app/helpers/repository_datatable_helper.rb b/app/helpers/repository_datatable_helper.rb
index f07546648..ba0175cc5 100644
--- a/app/helpers/repository_datatable_helper.rb
+++ b/app/helpers/repository_datatable_helper.rb
@@ -10,9 +10,10 @@ module RepositoryDatatableHelper
       row = {
             'DT_RowId': record.id,
             '1': assigned_row(record, assigned_rows),
-            '2': escape_input(record.name),
-            '3': I18n.l(record.created_at, format: :full),
-            '4': escape_input(record.created_by.full_name),
+            '2': record.id,
+            '3': escape_input(record.name),
+            '4': I18n.l(record.created_at, format: :full),
+            '5': escape_input(record.created_by.full_name),
             'recordEditUrl': Rails.application.routes.url_helpers
                                   .edit_repository_repository_row_path(
                                     repository,
diff --git a/app/models/concerns/searchable_model.rb b/app/models/concerns/searchable_model.rb
index 76f0aa89e..e2f7daf34 100644
--- a/app/models/concerns/searchable_model.rb
+++ b/app/models/concerns/searchable_model.rb
@@ -68,14 +68,24 @@ module SearchableModel
         end
       else
         unless attrs.empty?
+          id_index = 0 # quick fix to enable searching by repositoy_row id
           where_str =
             (attrs.map.with_index do |a, i|
-              "(trim_html_tags(#{a})) #{like} :t#{i} OR "
+              if a == 'repository_rows.id'
+                id_index = i
+                "#{a} = :t#{i} OR "
+              else
+                "(trim_html_tags(#{a})) #{like} :t#{i} OR "
+              end
             end
             ).join[0..-5]
           vals = (
             attrs.map.with_index do |_, i|
-              ["t#{i}".to_sym, "%#{sanitize_sql_like(query.to_s)}%"]
+              if id_index == i
+                ["t#{i}".to_sym, sanitize_sql_like(query).to_i]
+              else
+                ["t#{i}".to_sym, "%#{sanitize_sql_like(query.to_s)}%"]
+              end
             end
           ).to_h
 
diff --git a/app/models/my_module.rb b/app/models/my_module.rb
index e4677a97f..f38fa7b5e 100644
--- a/app/models/my_module.rb
+++ b/app/models/my_module.rb
@@ -343,6 +343,7 @@ class MyModule < ApplicationRecord
       .where(repository_id: repository_id)
       .order(created_at: order).find_each do |row|
       row_json = []
+      row_json << row.id
       row_json << row.name
       row_json << I18n.l(row.created_at, format: :full)
       row_json << row.created_by.full_name
@@ -351,6 +352,7 @@ class MyModule < ApplicationRecord
 
     # Prepare column headers
     headers = [
+      I18n.t('repositories.table.id'),
       I18n.t('repositories.table.row_name'),
       I18n.t('repositories.table.added_on'),
       I18n.t('repositories.table.added_by')
diff --git a/app/services/repository_datatable_service.rb b/app/services/repository_datatable_service.rb
index 55b815812..48c9935db 100644
--- a/app/services/repository_datatable_service.rb
+++ b/app/services/repository_datatable_service.rb
@@ -55,7 +55,9 @@ class RepositoryDatatableService
 
   def search(value)
     includes_json = { repository_cells: Extends::REPOSITORY_SEARCH_INCLUDES }
-    searchable_attributes = ['repository_rows.name', 'users.full_name'] +
+    searchable_attributes = ['repository_rows.name',
+                             'users.full_name',
+                             'repository_rows.id'] +
                             Extends::REPOSITORY_EXTRA_SEARCH_ATTR
 
     RepositoryRow.left_outer_joins(:created_by)
@@ -76,6 +78,7 @@ class RepositoryDatatableService
   def sortable_columns
     array = [
       'assigned',
+      'repository_rows.id',
       'repository_rows.name',
       'repository_rows.created_at',
       'users.full_name'
diff --git a/app/services/repository_zip_export.rb b/app/services/repository_zip_export.rb
index e192540fc..7ca6cda00 100644
--- a/app/services/repository_zip_export.rb
+++ b/app/services/repository_zip_export.rb
@@ -24,10 +24,12 @@ module RepositoryZipExport
                     when -1, -2
                       next
                     when -3
-                      I18n.t('repositories.table.row_name')
+                      I18n.t('repositories.table.id')
                     when -4
-                      I18n.t('repositories.table.added_by')
+                      I18n.t('repositories.table.row_name')
                     when -5
+                      I18n.t('repositories.table.added_by')
+                    when -6
                       I18n.t('repositories.table.added_on')
                     else
                       column = RepositoryColumn.find_by_id(c_id)
@@ -44,10 +46,12 @@ module RepositoryZipExport
                      when -1, -2
                        next
                      when -3
-                       row.name
+                       row.id
                      when -4
-                       row.created_by.full_name
+                       row.name
                      when -5
+                       row.created_by.full_name
+                     when -6
                        I18n.l(row.created_at, format: :full)
                      else
                        cell = row.repository_cells
diff --git a/app/views/repositories/_repository_row_info_modal.html.erb b/app/views/repositories/_repository_row_info_modal.html.erb
index 7f321e2c4..0747a9ccc 100644
--- a/app/views/repositories/_repository_row_info_modal.html.erb
+++ b/app/views/repositories/_repository_row_info_modal.html.erb
@@ -13,12 +13,17 @@
         </ol>
         <p>
           <span>
-            <%= t "repository_row.modal_info.added_on" %>
+            <%=t 'repository_row.modal_info.ID' %>
+            <%= @repository_row.id %>
+          </span>
+          <br>
+          <span>
+            <%= t "repository_row.modal_info.added_on" %>:
             <%= l @repository_row.created_at, format: :full %>
           </span>
           <br>
           <span>
-            <%= t "repository_row.modal_info.added_by" %>
+            <%= t "repository_row.modal_info.added_by" %>:
             <%= @repository_row.created_by.full_name %>
           </span>
           <% @repository_row.repository_cells.each do |repository_cell| %>
diff --git a/app/views/repositories/_repository_table.html.erb b/app/views/repositories/_repository_table.html.erb
index 85dfe7d57..aad7bcc3c 100644
--- a/app/views/repositories/_repository_table.html.erb
+++ b/app/views/repositories/_repository_table.html.erb
@@ -3,7 +3,7 @@
     data-current-uri="<%= request.original_url %>"
     data-repository-id="<%= repository.id %>"
     data-source="<%= repository_index_link %>"
-    data-num-columns="<%= 5 + repository.repository_columns.count %>"
+    data-num-columns="<%= 6 + repository.repository_columns.count %>"
     data-create-record="<%= repository_repository_rows_path(repository) %>"
     data-delete-record="<%= repository_delete_records_path(repository) %>"
     data-max-dropdown-length="<%= Constants::NAME_TRUNCATION_LENGTH_DROPDOWN %>"
@@ -16,6 +16,7 @@
       <tr>
         <th id="checkbox"><input name="select_all" value="1" type="checkbox"></th>
         <th id="assigned"><%= t("repositories.table.assigned") %></th>
+        <th id="row-id"><%= t("repositories.table.id") %></th>
         <th id="row-name"><%= t("repositories.table.row_name") %></th>
         <th id="added-on"><%= t("repositories.table.added_on") %></th>
         <th id="added-by"><%= t("repositories.table.added_by") %></th>
diff --git a/app/views/search/results/_repositories.html.erb b/app/views/search/results/_repositories.html.erb
index d403afe90..6bddd47f9 100644
--- a/app/views/search/results/_repositories.html.erb
+++ b/app/views/search/results/_repositories.html.erb
@@ -6,13 +6,11 @@
   </h5>
 
   <p>
-    <% repository_row.repository_cells.each do |cell| %>
-      <span>
-        <%=t "search.index.repositories.custom_column", column: cell.repository_column.name %>
-        <%= highlight cell.value.data, search_query.strip.split(/\s+/) %>
-      </span>
-      <br>
-    <% end %>
+    <span>
+      <%=t 'repository_row.modal_info.ID' %>
+      <%= repository_row.id %>
+    </span>
+    <br />
     <span>
       <%=t "search.index.repositories.added_on" %>
       <%=l repository_row.created_at, format: :full %>
@@ -22,6 +20,13 @@
       <%=t "search.index.repositories.added_by" %>
       <%= highlight repository_row.created_by.full_name, search_query.strip.split(/\s+/) %>
     </span>
+    <% repository_row.repository_cells.each do |cell| %>
+      <span>
+        <%=t "search.index.repositories.custom_column", column: cell.repository_column.name %>
+        <%= highlight cell.value.data, search_query.strip.split(/\s+/) %>
+      </span>
+      <br>
+    <% end %>
   </p>
 
   <p>
diff --git a/config/initializers/constants.rb b/config/initializers/constants.rb
index 6b0322c74..c3e67cd58 100644
--- a/config/initializers/constants.rb
+++ b/config/initializers/constants.rb
@@ -158,7 +158,7 @@ class Constants
   COLOR_DOVE_GRAY = '#666666'.freeze # $color-dove-gray
   COLOR_EMPEROR = '#555555'.freeze # $color-emperor
   COLOR_BLACK = '#000000'.freeze # $color-black
-  
+
 
   #=============================================================================
   # External URLs
@@ -842,17 +842,17 @@ class Constants
   REPOSITORY_TABLE_DEFAULT_STATE = {
     'time' => 0,
     'start' => 0,
-    'length' => 5,
-    'order' => [[2, 'desc']],
+    'length' => 6,
+    'order' => [[3, 'desc']],
     'search' => { 'search' => '',
                   'smart' => true,
                   'regex' => false,
                   'caseInsensitive' => true },
     'columns' => [],
     'assigned' => 'assigned',
-    'ColReorder' => [*0..4]
+    'ColReorder' => [*0..5]
   }
-  5.times do
+  6.times do
     REPOSITORY_TABLE_DEFAULT_STATE['columns'] << {
       'visible' => true,
       'search' => { 'search' => '',
diff --git a/config/locales/en.yml b/config/locales/en.yml
index bfb7bfb84..d77e82540 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -918,6 +918,7 @@ en:
       breadcrumbs:
         repositories: "Repositories"
     table:
+      id: 'ID'
       assigned: "Assigned"
       row_name: "Name"
       added_on: "Added on"
@@ -992,6 +993,7 @@ en:
 
   repository_row:
     modal_info:
+      ID: 'ID:'
       head_title: "Information for item '%{repository_row}'"
       added_on: "Added on"
       added_by: "Added by"

From 5eb007f4d280e02a082281b045e3842056ade145 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 4 Apr 2018 13:22:14 +0200
Subject: [PATCH 21/23] fixes per @mlorb 's request

---
 app/assets/stylesheets/themes/scinote.scss  |   1 -
 app/views/repositories/_repository.html.erb | 116 --------------------
 app/views/repositories/_sidebar.html.erb    |  12 +-
 app/views/repositories/index.html.erb       |   2 +-
 config/locales/en.yml                       |  12 +-
 5 files changed, 15 insertions(+), 128 deletions(-)
 delete mode 100644 app/views/repositories/_repository.html.erb

diff --git a/app/assets/stylesheets/themes/scinote.scss b/app/assets/stylesheets/themes/scinote.scss
index bf2b4b0cc..010d461e2 100644
--- a/app/assets/stylesheets/themes/scinote.scss
+++ b/app/assets/stylesheets/themes/scinote.scss
@@ -1,7 +1,6 @@
 @import 'constants';
 @import "mixins";
 @import "main_navigation";
-@import "buttons";
 @import "repositories";
 /** Layout **/
 
diff --git a/app/views/repositories/_repository.html.erb b/app/views/repositories/_repository.html.erb
deleted file mode 100644
index e9b36dd10..000000000
--- a/app/views/repositories/_repository.html.erb
+++ /dev/null
@@ -1,116 +0,0 @@
-<%= render partial: "repositories/delete_record_modal.html.erb" %>
-<%= render partial: "repositories/delete_column_modal.html.erb" %>
-<%= render partial: 'repositories/export_repository_modal.html.erb',
-           locals: { repository: repository } %>
-
-<div id="alert-container"></div>
-
-<div id="repository-toolbar">
-
-  <% if can_create_repository_rows?(repository.team) %>
-    <button type="button" class="btn btn-default editAdd" id="addRepositoryRecord" onclick="onClickAddRecord()">
-      <span class="glyphicon glyphicon-plus"></span>
-      <span class="hidden-xs"><%= t("repositories.add_new_record") %></span>
-    </button>
-    <button type="button" class="btn btn-default" id="importRecordsButton">
-      <span class="glyphicon glyphicon-cloud-upload"></span>
-      <span class="hidden-xs"><%= t('repositories.import_records.import') %></span>
-    </button>
-  <% end %>
-
-  <% if can_read_team?(repository.team) %>
-    <a href="#" class="btn btn-default" id="exportRepositoriesButton" data-turbolinks="false">
-      <span class="glyphicon glyphicon-cloud-download"></span>
-      <span class="hidden-xs"><%= t("my_modules.repository.export") %></span>
-    </a>
-  <% end %>
-
-  <div class="repository-cog">
-    <div class="dropdown">
-      <div class="btn btn-default"
-           type="button"
-           data-toggle="dropdown"
-           aria-haspopup="true"
-           aria-expanded="true"
-           <%= "disabled='disabled'" unless can_manage_repository?(repository) || can_create_repositories?(repository.team) %>>
-        <span class="glyphicon glyphicon-cog"></span>
-        <span class="caret"></span>
-      </div>
-      <% if can_manage_repository?(repository) || can_create_repositories?(repository.team) %>
-        <ul class="dropdown-menu pull-right">
-          <li class="dropdown-header">
-            <%= t("repositories.index.options_dropdown.header") %>
-          </li>
-          <% if can_manage_repository?(repository) %>
-            <li>
-              <%= link_to t('repositories.index.options_dropdown.rename'),
-                          team_repository_rename_modal_path(repository_id: repository),
-                          class: "rename-repo-option",
-                          remote: true %>
-            </li>
-          <% end %>
-          <% if can_create_repositories?(repository.team) %>
-            <li>
-              <%= link_to t('repositories.index.options_dropdown.copy'),
-                          team_repository_copy_modal_path(repository_id: repository),
-                          class: "copy-repo-option",
-                          remote: true %>
-            </li>
-          <% end %>
-          <% if can_manage_repository?(repository) %>
-            <li role="separator" class="divider"></li>
-            <li>
-              <%= link_to t('repositories.index.modal_delete.delete'),
-                          team_repository_destroy_modal_path(repository_id: repository),
-                          class: "delete-repo-option",
-                          remote: true %>
-            </li>
-          <% end %>
-        </ul>
-      <% end %>
-    </div>
-  </div>
-
-  <div id="datatables-buttons" style="display: inline;">
-    <%= render partial: "columns_reorder_dropdown", formats: :html %>
-  </div>
-</div>
-
-<div class="btn-group inline" id="saveCancel" data-toggle="buttons" style="display:none">
-  <button type="button" class="btn btn-primary" id="saveRecord" onclick="onClickSave()">
-    <span class="glyphicon glyphicon-save"></span>
-    <%= t("repositories.save_record") %>
-  </button>
-  <button type="button" class="btn btn-default" id="cancelSave" onclick="onClickCancel()">
-    <span class="glyphicon glyphicon-remove visible-xs-inline"></span>
-    <span class="hidden-xs"><%= t("repositories.cancel_save") %></span>
-  </button>
-</div>
-
-<!-- These buttons are appended to table in javascript, after table initialization -->
-<div class="toolbarButtons" style="display:none">
-  <button type="button" class="btn btn-default editAdd" id="editRepositoryRecord" onclick="onClickEdit()" disabled>
-    <span class="glyphicon glyphicon-pencil"></span>
-    <span class="hidden-xs-custom"><%= t("repositories.edit_record") %></span>
-  </button>
-
-  <% if can_manage_repository_rows?(repository.team) %>
-    <button type="button" class="btn btn-default"
-      id="deleteRepositoryRecordsButton" data-target="#deleteRepositoryRecord" data-toggle="modal" disabled>
-      <span class="glyphicon glyphicon-trash"></span>
-      <span class="hidden-xs-custom"><%= t'repositories.delete_record' %></span>
-        <%= submit_tag I18n.t('repositories.delete_record'), :class => "hidden
-        delete_repository_records_submit" %>
-    </button>
-  <% end %>
-</div>
-
-<%= render partial: "repositories/repository_table.html.erb",
-           locals: {
-             repository: repository,
-             repository_index_link: repository_table_index_path(repository)
-           }
-%>
-<%= render partial: 'repositories/import_repository_records_modal.html.erb',
-                    locals: { repository: repository } %>
-<%= javascript_include_tag 'repositories/edit', 'data-turbolinks-track' => true %>
diff --git a/app/views/repositories/_sidebar.html.erb b/app/views/repositories/_sidebar.html.erb
index e5fa31153..3651d48cc 100644
--- a/app/views/repositories/_sidebar.html.erb
+++ b/app/views/repositories/_sidebar.html.erb
@@ -9,11 +9,15 @@
         </li>
         <% repositories.each do |repository| %>
           <% cache repository do %>
-            <li class="<%= 'active' if current_page?(repository_path(repository)) %>" >
+            <li class="<%= 'active parent_li' if current_page?(repository_path(repository)) %>" >
               <span class="tree-link line-wrap no-indent">
-                <%= link_to repository.name,
-                            repository_path(repository),
-                            data: { 'no-turbolink' => 'true' } %>
+                <% if current_page?(repository_path(repository)) %>
+                <span title="<%= repository.name %>"><%= repository.name %></span>
+                <% else %>
+                  <%= link_to repository.name,
+                              repository_path(repository),
+                              data: { 'no-turbolink' => 'true' } %>
+                <% end %>
               </span>
             </li>
           <% end %>
diff --git a/app/views/repositories/index.html.erb b/app/views/repositories/index.html.erb
index 960f77ea1..c9001ad32 100644
--- a/app/views/repositories/index.html.erb
+++ b/app/views/repositories/index.html.erb
@@ -12,7 +12,7 @@
     <br />
     <%= link_to t('libraries.index.no_libraries.create_new_button'),
                 create_modal_team_repositories_path(current_team),
-                class: "btn btn-info btn-lg",
+                class: "btn btn-primary btn-lg",
                 id: "create-new-repository",
                 remote: true %>
   </div>
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 74f24836e..cb41cdfe5 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -992,15 +992,15 @@ en:
 
   libraries:
     sidebar:
-      title: "Libraries"
+      title: "Inventories"
     index:
-      head_title: "Libraries"
+      head_title: "Inventories"
       no_libraries:
-        text: "You don't have any libraries."
-        title: "Please create your first Library"
-        create_new_button: "Create New Library"
+        text: "You don't have any inventories."
+        title: "Please create your first Inventory"
+        create_new_button: "Create New Inventory"
     show:
-      head_title: "Libraries | %{library}"
+      head_title: "Inventories | %{library}"
   repository_row:
     modal_info:
       head_title: "Information for item '%{repository_row}'"

From 6e255a465761de29ec12da8486a842c27e74d325 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 4 Apr 2018 14:44:32 +0200
Subject: [PATCH 22/23] fixes failing specs

---
 app/models/concerns/searchable_model.rb              |  9 +++++----
 spec/controllers/repository_rows_controller_spec.rb  | 12 ++++++------
 spec/services/repository_datatable_service_spec.rb   | 12 ++++++------
 .../api/schemas/repository_row_datatables.json       |  5 +++--
 4 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/app/models/concerns/searchable_model.rb b/app/models/concerns/searchable_model.rb
index e2f7daf34..20d80fed9 100644
--- a/app/models/concerns/searchable_model.rb
+++ b/app/models/concerns/searchable_model.rb
@@ -68,12 +68,13 @@ module SearchableModel
         end
       else
         unless attrs.empty?
-          id_index = 0 # quick fix to enable searching by repositoy_row id
+          # quick fix to enable searching by repositoy_row id
+          id_index = { present: false }
           where_str =
             (attrs.map.with_index do |a, i|
               if a == 'repository_rows.id'
-                id_index = i
-                "#{a} = :t#{i} OR "
+                id_index = { present: true, val: i }
+                "(#{a}) = :t#{i} OR "
               else
                 "(trim_html_tags(#{a})) #{like} :t#{i} OR "
               end
@@ -81,7 +82,7 @@ module SearchableModel
             ).join[0..-5]
           vals = (
             attrs.map.with_index do |_, i|
-              if id_index == i
+              if id_index[:present] && id_index[:val] == i
                 ["t#{i}".to_sym, sanitize_sql_like(query).to_i]
               else
                 ["t#{i}".to_sym, "%#{sanitize_sql_like(query.to_s)}%"]
diff --git a/spec/controllers/repository_rows_controller_spec.rb b/spec/controllers/repository_rows_controller_spec.rb
index 0ee849e91..feb487cb0 100644
--- a/spec/controllers/repository_rows_controller_spec.rb
+++ b/spec/controllers/repository_rows_controller_spec.rb
@@ -62,7 +62,7 @@ describe RepositoryRowsController, type: :controller do
 
     describe 'json object' do
       it 'returns a valid object' do
-        params = { order: { 0 => { column: '3', dir: 'asc' } },
+        params = { order: { 0 => { column: '4', dir: 'asc' } },
                    drow: '0',
                    search: { value: '' },
                    length: '10',
@@ -77,7 +77,7 @@ describe RepositoryRowsController, type: :controller do
 
     describe 'pagination' do
       it 'returns first 10 records' do
-        params = { order: { 0 => { column: '3', dir: 'asc' } },
+        params = { order: { 0 => { column: '4', dir: 'asc' } },
                    drow: '0',
                    search: { value: '' },
                    length: '10',
@@ -86,11 +86,11 @@ describe RepositoryRowsController, type: :controller do
         get :index, params: params, format: :json
         response_body = JSON.parse(response.body)
         expect(response_body['data'].length).to eq 10
-        expect(response_body['data'].first['2']).to eq 'row (0)'
+        expect(response_body['data'].first['3']).to eq 'row (0)'
       end
 
       it 'returns next 10 records' do
-        params = { order: { 0 => { column: '3', dir: 'asc' } },
+        params = { order: { 0 => { column: '4', dir: 'asc' } },
                    drow: '0',
                    search: { value: '' },
                    length: '10',
@@ -99,11 +99,11 @@ describe RepositoryRowsController, type: :controller do
         get :index, params: params, format: :json
         response_body = JSON.parse(response.body)
         expect(response_body['data'].length).to eq 10
-        expect(response_body['data'].first['2']).to eq 'row (10)'
+        expect(response_body['data'].first['3']).to eq 'row (10)'
       end
 
       it 'returns first 25 records' do
-        params = { order: { 0 => { column: '2', dir: 'desc' } },
+        params = { order: { 0 => { column: '4', dir: 'desc' } },
                    drow: '0',
                    search: { value: '' },
                    length: '25',
diff --git a/spec/services/repository_datatable_service_spec.rb b/spec/services/repository_datatable_service_spec.rb
index e32b13f19..2a5f9816a 100644
--- a/spec/services/repository_datatable_service_spec.rb
+++ b/spec/services/repository_datatable_service_spec.rb
@@ -52,7 +52,7 @@ describe RepositoryDatatableService do
 
   context 'object' do
     let(:params) do
-      { order: { 0 => { column: '2', dir: 'asc' } },
+      { order: { 0 => { column: '3', dir: 'asc' } },
         search: { value: 'row' } }
     end
 
@@ -65,7 +65,7 @@ describe RepositoryDatatableService do
         contitions = subject.send(:build_conditions, params)
         expect(contitions[:search_value]).to eq 'row'
         expect(contitions[:order_by_column]).to eq(
-          { column: 2, dir: 'asc' }
+          { column: 3, dir: 'asc' }
         )
       end
     end
@@ -73,7 +73,7 @@ describe RepositoryDatatableService do
     describe '#sortable_columns' do
       it 'returns an array of all columns that are sortable' do
         columns = subject.send(:sortable_columns)
-        expect(columns.length).to eq 5
+        expect(columns.length).to eq 6
       end
     end
 
@@ -92,7 +92,7 @@ describe RepositoryDatatableService do
 
   describe 'ordering' do
     it 'is ordered by row name asc' do
-      params = { order: { 0 => { column: '2', dir: 'asc' } },
+      params = { order: { 0 => { column: '3', dir: 'asc' } },
                  search: { value: '' } }
       subject = RepositoryDatatableService.new(repository,
                                                params,
@@ -102,7 +102,7 @@ describe RepositoryDatatableService do
     end
 
     it 'is ordered by row name desc' do
-      params = { order: { 0 => { column: '2', dir: 'desc' } },
+      params = { order: { 0 => { column: '3', dir: 'desc' } },
                  search: { value: '' } }
       subject = RepositoryDatatableService.new(repository,
                                                params,
@@ -121,7 +121,7 @@ describe RepositoryDatatableService do
     end
 
     it 'returns only the searched entity' do
-      params = { order: { 0 => { column: '2', dir: 'desc' } },
+      params = { order: { 0 => { column: '4', dir: 'desc' } },
                  search: { value: 'test' } }
       subject = RepositoryDatatableService.new(repository,
                                                params,
diff --git a/spec/support/api/schemas/repository_row_datatables.json b/spec/support/api/schemas/repository_row_datatables.json
index 0a73d82f6..5c209e998 100644
--- a/spec/support/api/schemas/repository_row_datatables.json
+++ b/spec/support/api/schemas/repository_row_datatables.json
@@ -8,13 +8,14 @@
     "data": {
       "type": "array",
       "items":{
-        "required": ["DT_RowId", "1", "2", "3", "4", "recordEditUrl", "recordUpdateUrl", "recordInfoUrl"],
+        "required": ["DT_RowId", "1", "2", "3", "4", "5", "recordEditUrl", "recordUpdateUrl", "recordInfoUrl"],
         "properties": {
           "DT_RowId": { "type": "integer" },
           "1": { "type": "string" },
-          "2": { "type": "string" },
+          "2": { "type": "integer" },
           "3": { "type": "string" },
           "4": { "type": "string" },
+          "5": { "type": "string" },
           "recordEditUrl": { "type": "string" },
           "recordUpdateUrl": { "type": "string" },
           "recordInfoUrl": { "type": "string" }

From 77f80271dd4e4997c960c39c2148ad097e5287b2 Mon Sep 17 00:00:00 2001
From: zmagod <zmago_devetak@yahoo.com>
Date: Wed, 4 Apr 2018 14:52:59 +0200
Subject: [PATCH 23/23] fixes per @mojca 's request

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

diff --git a/config/locales/en.yml b/config/locales/en.yml
index 7ea2f1f0b..979453ad5 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -1845,7 +1845,7 @@ en:
     expired_description: 'Please export the data again in order to receive a new link.'
     modal_label: 'Export request received'
     modal_html: "<p>Your export request is being processed.</p><p>When completed we will <strong>send an email to %{email}</strong> inbox with a link to your exported samples. Note that the link will expire in 7 days.</p>"
-    repository_header_html: 'You are about to export selected items in inventory %{repository}'
+    repository_header_html: 'You are about to export selected items in inventory %{repository}.'
     files_alert: 'Files uploaded to inventory items will not be exported. Only filenames will be exported.'
     repository_footer_html: 'Inventory will be exported in a .csv file format. You will receive <strong>email with a link</strong> where you can download it.'
     export_error: "Error when creating zip export."