Merge pull request #216 from portagenetwork/integration

3.0.4+portage-3.0.13 release
portagenetwork · Jul 13, 2022 · 6e78e09 · 6e78e09
2 parents da9f7c2 + fa57c99
commit 6e78e09
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diff --git a/.github/workflows/brakeman.yml b/.github/workflows/brakeman.yml
@@ -15,6 +15,6 @@ jobs:
     - name: Brakeman
       uses: artplan1/[email protected]
       with:
-        flags: "--color"
+        flags: "--no-exit-on-warn" # OPTIONAL: change this no-exit-on-warn flag to avoid complaining of EOL security warning
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,35 @@
 # Changelog
 
+## [3.0.4+portage-3.0.13] - 2022-07-13
+
+### Changed
+
+- Upgraded Rails to 5.2.8.1 to fix the Possible RCE escalation bug with Serialized Columns in Active Record in Rails 5.2.6 (https://groups.google.com/g/rubyonrails-security/c/MmFO3LYQE8U/m/q9axtXheAQAJ)
+
+- Along with the Rails upgrade, upgraded activejob, activeview, activemodal, activestorage, activepack, activerecord, activesupport, actioncable, actionmailer, actionjob, actionview and railsties to 5.2.8.1
+
+- Along with the Rails upgrade, upgraded i18n to 1.8.11
+
+- Along with the Rails upgrade, upgraded rack to 2.2.4
+
+- Along with the Rails upgrade, upgraded sprockets to 4.0.3
+
+- Along with the Rails upgrade, upgraded  marcel to 1.0.2
+
+- Along with the Rails upgrade, upgraded mini_mine to 1.1.2
+
+- Along with the Rails upgrade, upgraded concurrent-ruby to 1.1.10
+
+### Added
+
+- Added contributors to the plan's cover page (if there is any) [#202](https://github.com/portagenetwork/roadmap/issues/202)
+
+- Added plan title to CSV exported file
+
+### Fixed
+
+- Added bootstrap-select stylesheet back after version 3 upgrade to fix the option-picker UI bug [#195](https://github.com/portagenetwork/roadmap/issues/195)
+
 ## [3.0.4+portage-3.0.12] - 2022-05-12
 
 ### Added

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -9,45 +9,45 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actioncable (5.2.6)
-      actionpack (= 5.2.6)
+    actioncable (5.2.8.1)
+      actionpack (= 5.2.8.1)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailer (5.2.6)
-      actionpack (= 5.2.6)
-      actionview (= 5.2.6)
-      activejob (= 5.2.6)
+    actionmailer (5.2.8.1)
+      actionpack (= 5.2.8.1)
+      actionview (= 5.2.8.1)
+      activejob (= 5.2.8.1)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (5.2.6)
-      actionview (= 5.2.6)
-      activesupport (= 5.2.6)
+    actionpack (5.2.8.1)
+      actionview (= 5.2.8.1)
+      activesupport (= 5.2.8.1)
       rack (~> 2.0, >= 2.0.8)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.2)
-    actionview (5.2.6)
-      activesupport (= 5.2.6)
+    actionview (5.2.8.1)
+      activesupport (= 5.2.8.1)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.0.3)
-    activejob (5.2.6)
-      activesupport (= 5.2.6)
+    activejob (5.2.8.1)
+      activesupport (= 5.2.8.1)
       globalid (>= 0.3.6)
-    activemodel (5.2.6)
-      activesupport (= 5.2.6)
-    activerecord (5.2.6)
-      activemodel (= 5.2.6)
-      activesupport (= 5.2.6)
+    activemodel (5.2.8.1)
+      activesupport (= 5.2.8.1)
+    activerecord (5.2.8.1)
+      activemodel (= 5.2.8.1)
+      activesupport (= 5.2.8.1)
       arel (>= 9.0)
     activerecord-nulldb-adapter (0.7.0)
       activerecord (>= 5.2.0, < 6.3)
-    activestorage (5.2.6)
-      actionpack (= 5.2.6)
-      activerecord (= 5.2.6)
+    activestorage (5.2.8.1)
+      actionpack (= 5.2.8.1)
+      activerecord (= 5.2.8.1)
       marcel (~> 1.0.0)
-    activesupport (5.2.6)
+    activesupport (5.2.8.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -111,7 +111,7 @@ GEM
       open4 (~> 1.3)
     coderay (1.1.3)
     colored2 (3.1.2)
-    concurrent-ruby (1.1.9)
+    concurrent-ruby (1.1.10)
     contact_us (1.2.0)
       rails (>= 4.2.0)
     cork (0.3.0)
@@ -247,7 +247,7 @@ GEM
     httparty (0.18.1)
       mime-types (~> 3.0)
       multi_xml (>= 0.5.2)
-    i18n (1.8.10)
+    i18n (1.8.11)
       concurrent-ruby (~> 1.0)
     ipaddress (0.8.3)
     jbuilder (2.11.2)
@@ -284,16 +284,16 @@ GEM
     lumberjack (1.2.8)
     mail (2.7.1)
       mini_mime (>= 0.1.1)
-    marcel (1.0.1)
+    marcel (1.0.2)
     method_source (1.0.0)
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2021.0704)
     mimemagic (0.3.10)
       nokogiri (~> 1)
       rake
-    mini_mime (1.1.0)
-    mini_portile2 (2.8.0)
+    mini_mime (1.1.2)
+    mini_portile2 (2.5.3)
     minitest (5.14.4)
     mocha (1.13.0)
     msgpack (1.4.2)
@@ -355,8 +355,8 @@ GEM
       activesupport (>= 3.0.0)
     pundit-matchers (1.7.0)
       rspec-rails (>= 3.0.0)
-    racc (1.6.0)
-    rack (2.2.3.1)
+    racc (1.5.2)
+    rack (2.2.4)
     rack-mini-profiler (2.3.2)
       rack (>= 1.2.0)
     rack-protection (2.1.0)
@@ -365,18 +365,18 @@ GEM
       rack
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
-    rails (5.2.6)
-      actioncable (= 5.2.6)
-      actionmailer (= 5.2.6)
-      actionpack (= 5.2.6)
-      actionview (= 5.2.6)
-      activejob (= 5.2.6)
-      activemodel (= 5.2.6)
-      activerecord (= 5.2.6)
-      activestorage (= 5.2.6)
-      activesupport (= 5.2.6)
+    rails (5.2.8.1)
+      actioncable (= 5.2.8.1)
+      actionmailer (= 5.2.8.1)
+      actionpack (= 5.2.8.1)
+      actionview (= 5.2.8.1)
+      activejob (= 5.2.8.1)
+      activemodel (= 5.2.8.1)
+      activerecord (= 5.2.8.1)
+      activestorage (= 5.2.8.1)
+      activesupport (= 5.2.8.1)
       bundler (>= 1.3.0)
-      railties (= 5.2.6)
+      railties (= 5.2.8.1)
       sprockets-rails (>= 2.0.0)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
@@ -387,9 +387,9 @@ GEM
       nokogiri (>= 1.6)
     rails-html-sanitizer (1.4.3)
       loofah (~> 2.3)
-    railties (5.2.6)
-      actionpack (= 5.2.6)
-      activesupport (= 5.2.6)
+    railties (5.2.8.1)
+      actionpack (= 5.2.8.1)
+      activesupport (= 5.2.8.1)
       method_source
       rake (>= 0.8.7)
       thor (>= 0.19.0, < 2.0)
@@ -508,7 +508,7 @@ GEM
     spring-watcher-listen (2.0.1)
       listen (>= 2.7, < 4.0)
       spring (>= 1.2, < 3.0)
-    sprockets (4.0.2)
+    sprockets (4.0.3)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
     sprockets-rails (3.2.2)
@@ -653,4 +653,4 @@ RUBY VERSION
    ruby 2.6.3p62
 
 BUNDLED WITH
-   2.3.6
+   2.3.12
diff --git a/app/assets/stylesheets/application.scss b/app/assets/stylesheets/application.scss
@@ -4,7 +4,7 @@
 
 // Pull in the webpacker managed copy of Bootstrap Stylesheets
 @import "../../../node_modules/bootstrap-sass/assets/stylesheets/_bootstrap.scss";
-// @import "../../../node_modules/bootstrap-select/sass/bootstrap-select.scss";
+@import "../../../node_modules/bootstrap-select/sass/bootstrap-select.scss";
 
 @import "blocks/*";
 @import "utils/*";

diff --git a/app/controllers/plan_exports_controller.rb b/app/controllers/plan_exports_controller.rb
@@ -33,11 +33,11 @@ def show
 
     @hash           = @plan.as_pdf(current_user, @show_coversheet)
     @formatting     = export_params[:formatting] || @plan.settings(:export).formatting
-    
-    if params.key?(:phase_id) && params[:phase_id].length > 0
+
+    if params.key?(:phase_id) && params[:phase_id].length.positive?
       # order phases by phase number asc
-      @hash[:phases] = @hash[:phases].sort_by{|phase| phase[:number]}
-      if (params[:phase_id] == "All")
+      @hash[:phases] = @hash[:phases].sort_by { |phase| phase[:number] }
+      if params[:phase_id] == "All"
         @hash[:all_phases] = true
       else
         @selected_phase = @plan.phases.find(params[:phase_id])
@@ -46,6 +46,14 @@ def show
       @selected_phase = @plan.phases.order("phases.updated_at DESC")
                              .detect { |p| p.visibility_allowed?(@plan) }
     end
+
+    # Added contributors to coverage of plans.
+    # Users will see both roles and contributor names if the role is filled
+    @hash[:data_curation] = Contributor.where(plan_id: @plan.id).data_curation
+    @hash[:investigation] = Contributor.where(plan_id: @plan.id).investigation
+    @hash[:pa] =  Contributor.where(plan_id: @plan.id).project_administration
+    @hash[:other] = Contributor.where(plan_id: @plan.id).other
+
     respond_to do |format|
       format.html { show_html }
       format.csv  { show_csv }
@@ -93,8 +101,8 @@ def show_pdf
                date: l(@plan.updated_at.to_date, format: :readable)
              },
              font_size: 8,
-             spacing:   (Integer(@formatting[:margin][:bottom]) / 2) - 4,
-             right:     _("[page] of [topage]"),
+             spacing: (Integer(@formatting[:margin][:bottom]) / 2) - 4,
+             right: _("[page] of [topage]"),
              encoding: "UTF-8"
            }
   end

diff --git a/app/models/concerns/exportable_plan.rb b/app/models/concerns/exportable_plan.rb
@@ -102,6 +102,13 @@ def prepare_coversheet
     end
     hash[:attribution] = attribution
 
+    # Added contributors to coverage of plans.
+    # Users will see both roles and contributor names if the role is filled
+    hash[:data_curation] = Contributor.where(plan_id: id).data_curation
+    hash[:investigation] = Contributor.where(plan_id: id).investigation
+    hash[:pa] =  Contributor.where(plan_id: id).project_administration
+    hash[:other] = Contributor.where(plan_id: id).other
+
     # Org name of plan owner's org
     hash[:affiliation] = owner.present? ? owner.org.name : ""
 
@@ -127,12 +134,27 @@ def prepare_coversheet
 
   # rubocop:disable Metrics/MethodLength, Metrics/AbcSize
   def prepare_coversheet_for_csv(csv, _headings, hash)
+    csv << [_("Title: "), _("%{title}") % { title: title }]
     csv << [if hash[:attribution].many?
               _("Creators: ")
             else
               _("Creator:")
             end, _("%{authors}") % { authors: hash[:attribution].join(", ") }]
-    csv << ["Affiliation: ", _("%{affiliation}") % { affiliation: hash[:affiliation] }]
+    if hash[:investigation].present?
+      csv << [_("Principal Investigator: "),
+              _("%{investigation}") % { investigation: hash[:investigation].map(&:name).join(", ") }]
+    end
+    if hash[:data_curation].present?
+      csv << [_("Date Manager: "),
+              _("%{data_curation}") % { data_curation: hash[:data_curation].map(&:name).join(", ") }]
+    end
+    if hash[:pa].present?
+      csv << [_("Project Administrator: "), _("%{pa}") % { pa: hash[:pa].map(&:name).join(", ") }]
+    end
+    if hash[:other].present?
+      csv << [_("Contributor: "), _("%{other}") % { other: hash[:other].map(&:name).join(", ") }]
+    end
+    csv << [_("Affiliation: "), _("%{affiliation}") % { affiliation: hash[:affiliation] }]
     csv << if hash[:funder].present?
              [_("Template: "), _("%{funder}") % { funder: hash[:funder] }]
            else

diff --git a/app/views/shared/export/_plan_coversheet.erb b/app/views/shared/export/_plan_coversheet.erb
@@ -7,6 +7,22 @@
   <%# Allow raw html (==) for plan_attribution as it has <b> tags %>
   <p><%== plan_attribution(@hash[:attribution]) %></p><br>
 
+  <%# Added contributors to coverage of plans. 
+    # Users will see both roles and contributor names if the role is filled %>
+  <%# Roles are ranked by PI -> DM -> PA -> Other (if any) %>
+  <% if @hash[:investigation].present? %>
+  <p><b><%= _("Principal Investigator: ") %></b><%= @hash[:investigation].map(&:name).join(', ') %></p><br>
+  <% end %>
+  <% if @hash[:data_curation].present? %>
+  <p><b><%= _("Data Manager: ") %></b><%= @hash[:data_curation].map(&:name).join(', ') %></p><br>
+  <% end %>
+  <% if @hash[:pa].present? %>
+  <p><b><%= _("Project Administrator: ") %></b><%= @hash[:pa].map(&:name).join(', ') %></p><br>
+  <% end %>
+  <% if @hash[:other].present? %>
+  <p><b><%= _("Contributor: ") %></b><%= @hash[:other].map(&:name).join(', ') %></p><br>
+  <% end %>
+
   <p><b><%= _("Affiliation: ") %></b><%= @hash[:affiliation] %></p><br>
 
   <% if @hash[:funder].present? %>

diff --git a/app/views/shared/export/_plan_txt.erb b/app/views/shared/export/_plan_txt.erb
@@ -1,7 +1,23 @@
 <%= "#{@plan.title}" %>
 <%= "----------------------------------------------------------\n" %>
 <% if @show_coversheet %>
+
 <%= @hash[:attribution].many? ? _("Creators: ") : _('Creator:') %> <%= @hash[:attribution].join(', ') %>
+<%# Added contributors to coverage of plans. 
+    # Users will see both roles and contributor names if the role is filled %>
+<%# Roles are ranked by PI -> DM -> PA -> Other (if any) %>
+  <% if @hash[:investigation].present? %>
+<%= _("Principal Investigator: ") + @hash[:investigation].map(&:name).join(', ') %>
+  <% end %>
+  <% if @hash[:data_curation].present? %>
+<%= _("Data Manager: ") +  @hash[:data_curation].map(&:name).join(', ') %>
+  <% end %>
+  <% if @hash[:pa].present? %>
+<%= _("Project Administrator: ") + @hash[:pa].map(&:name).join(', ') %>
+  <% end %>
+  <% if @hash[:other].present? %>
+<%= _("Contributor: ") + @hash[:other].map(&:name).join(', ') %>
+  <% end %>
 <%= _("Affiliation: ") + @hash[:affiliation] %>
   <% if @hash[:funder].present? %>
 <%= _("Template: ") + @hash[:funder] %>