From 1f19808d78e5586e10b0ce89f91b531964cd60cf Mon Sep 17 00:00:00 2001 From: Stephen Hulme Date: Fri, 20 Mar 2026 14:35:07 +0000 Subject: [PATCH 1/6] fix: improve readbility of study specification page --- .../stylesheets/all/sequencescape.scss | 9 +++++ app/views/studies/properties.html.erb | 35 +++++++++---------- 2 files changed, 26 insertions(+), 18 deletions(-) diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss index f385b3be1c..ac89f999c5 100644 --- a/app/frontend/stylesheets/all/sequencescape.scss +++ b/app/frontend/stylesheets/all/sequencescape.scss @@ -823,6 +823,15 @@ td.qc_pass { background-color: #ff8; } +#template_form_body table { + @extend .mb-2 +} + +#template_form_body td { + vertical-align: top; + line-height: 1.1em; +} + #plate td.selected { background-color: #72cf3f; } diff --git a/app/views/studies/properties.html.erb b/app/views/studies/properties.html.erb index 2dabc1e796..d3c2dda9c9 100644 --- a/app/views/studies/properties.html.erb +++ b/app/views/studies/properties.html.erb @@ -7,28 +7,27 @@ <% add :back_menu, I18n.t("navigation.menu.back_to_study") => study_path(@study) -%>
- <%= link_to "View status", study_path(@study) %> + <%= link_to "View samples status", study_path(@study) %>

Study Specification

- - - - - - - - - - - - - - - -
Name:<%=h @study.name %>
Created at:<%=h @study.created_at.to_formatted_s(:day_full_with_time) %>
Study reference genome:<%= @study.study_metadata.reference_genome&.name %>
-
+ + + + + + + + + + + + + + + +
Name:<%=h @study.name %>
Created at:<%=h @study.created_at.to_formatted_s(:day_full_with_time) %>
Study reference genome:<%= @study.study_metadata.reference_genome&.name %>
<%= render partial: 'shared/metadata/show/study', locals: { study: @study } %>
From 42146c1a396cf649ee3708c2836ffbff75a1a3f6 Mon Sep 17 00:00:00 2001 From: Stephen Hulme Date: Fri, 20 Mar 2026 16:08:14 +0000 Subject: [PATCH 2/6] feat: add study accessioning checklist to properties page --- app/views/studies/properties.html.erb | 48 ++++++++++++++++----------- 1 file changed, 29 insertions(+), 19 deletions(-) diff --git a/app/views/studies/properties.html.erb b/app/views/studies/properties.html.erb index d3c2dda9c9..f9d770049e 100644 --- a/app/views/studies/properties.html.erb +++ b/app/views/studies/properties.html.erb @@ -9,25 +9,35 @@
<%= link_to "View samples status", study_path(@study) %>
+
+
+

Study Specification

-

Study Specification

+
+ + + + + + + + + + + + + + + +
Name:<%=h @study.name %>
Created at:<%=h @study.created_at.to_formatted_s(:day_full_with_time) %>
Study reference genome:<%= @study.study_metadata.reference_genome&.name %>
+ <%= render partial: 'shared/metadata/show/study', locals: { study: @study } %> +
+
+
-
- - - - - - - - - - - - - - - -
Name:<%=h @study.name %>
Created at:<%=h @study.created_at.to_formatted_s(:day_full_with_time) %>
Study reference genome:<%= @study.study_metadata.reference_genome&.name %>
- <%= render partial: 'shared/metadata/show/study', locals: { study: @study } %> +
+
Study Accessioning Checklist
+
+ <%= render partial: 'studies/information/study_accession_checklist' %> +
From ed8aa6eb6aff960e3daccf301422ef588dd45988 Mon Sep 17 00:00:00 2001 From: Stephen Hulme Date: Fri, 20 Mar 2026 16:08:26 +0000 Subject: [PATCH 3/6] fix: update links on properties page --- app/views/studies/properties.html.erb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/app/views/studies/properties.html.erb b/app/views/studies/properties.html.erb index f9d770049e..f6385acb13 100644 --- a/app/views/studies/properties.html.erb +++ b/app/views/studies/properties.html.erb @@ -4,11 +4,12 @@ <% if can? :edit, @study %> <% add :menu, "Edit" => edit_study_path(@study) -%> <% end %> +<% if can? :administer, @study %> + <% add :menu, "Manage" => url_for(controller: "admin/studies", action: "show", id: @study.id) -%> +<% end %> +<% add :menu, "View samples status" => study_path(@study) -%> <% add :back_menu, I18n.t("navigation.menu.back_to_study") => study_path(@study) -%> -
- <%= link_to "View samples status", study_path(@study) %> -

Study Specification

From 076665043757da4e651db48b125266fcb0d21bb0 Mon Sep 17 00:00:00 2001 From: Stephen Hulme Date: Fri, 20 Mar 2026 16:09:10 +0000 Subject: [PATCH 4/6] fix: update sample message with link to checklist --- app/helpers/samples_helper.rb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/app/helpers/samples_helper.rb b/app/helpers/samples_helper.rb index 9cb4cfbbcd..9e75a388a1 100644 --- a/app/helpers/samples_helper.rb +++ b/app/helpers/samples_helper.rb @@ -36,7 +36,9 @@ def should_be_accessioned_warning(sample) def no_accessionable_studies_warning(sample) accession_warning( 'Sample cannot be accessioned:', - sample.studies.map { |study| "Study '#{link(study)}' is missing an accession number" } + sample.studies.map do |study| # Add list item for each study + "Study '#{link(study)}' is not accessionable - #{accessioning_checklist_link(study)}" + end ) end @@ -65,4 +67,8 @@ def accession_warning(message, items) def link(study) link_to(ERB::Util.html_escape(study.name), study_path(study)) end + + def accessioning_checklist_link(study) + link_to 'view accessioning checklist', properties_study_path(study, anchor: 'study-accessioning-checklist') + end end From 9b1b1d89b18d9c41f75f789da3688d6ecf185a5d Mon Sep 17 00:00:00 2001 From: Stephen Hulme Date: Fri, 20 Mar 2026 16:48:57 +0000 Subject: [PATCH 5/6] style: lint --- app/frontend/stylesheets/all/sequencescape.scss | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/frontend/stylesheets/all/sequencescape.scss b/app/frontend/stylesheets/all/sequencescape.scss index ac89f999c5..9cae7195e9 100644 --- a/app/frontend/stylesheets/all/sequencescape.scss +++ b/app/frontend/stylesheets/all/sequencescape.scss @@ -824,7 +824,7 @@ td.qc_pass { } #template_form_body table { - @extend .mb-2 + @extend .mb-2; } #template_form_body td { From 6380142f0aa8d095d642c68785ed8e478fc45f09 Mon Sep 17 00:00:00 2001 From: Stephen Hulme Date: Tue, 31 Mar 2026 17:06:07 +0100 Subject: [PATCH 6/6] fix: remove extranous link to study --- app/views/studies/properties.html.erb | 1 - 1 file changed, 1 deletion(-) diff --git a/app/views/studies/properties.html.erb b/app/views/studies/properties.html.erb index f6385acb13..5f09d52620 100644 --- a/app/views/studies/properties.html.erb +++ b/app/views/studies/properties.html.erb @@ -7,7 +7,6 @@ <% if can? :administer, @study %> <% add :menu, "Manage" => url_for(controller: "admin/studies", action: "show", id: @study.id) -%> <% end %> -<% add :menu, "View samples status" => study_path(@study) -%> <% add :back_menu, I18n.t("navigation.menu.back_to_study") => study_path(@study) -%>