Merge branch 'main' into updated-deprecated-actions

seek4science · Mar 4, 2024 · 43da186 · 43da186
2 parents 6b69d76 + d18adb0
commit 43da186
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diff --git a/Gemfile.lock b/Gemfile.lock
@@ -51,40 +51,40 @@ GEM
   remote: https://rubygems.org/
   specs:
     RedCloth (4.3.3)
-    actioncable (6.1.7.6)
-      actionpack (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    actioncable (6.1.7.7)
+      actionpack (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (6.1.7.6)
-      actionpack (= 6.1.7.6)
-      activejob (= 6.1.7.6)
-      activerecord (= 6.1.7.6)
-      activestorage (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    actionmailbox (6.1.7.7)
+      actionpack (= 6.1.7.7)
+      activejob (= 6.1.7.7)
+      activerecord (= 6.1.7.7)
+      activestorage (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       mail (>= 2.7.1)
-    actionmailer (6.1.7.6)
-      actionpack (= 6.1.7.6)
-      actionview (= 6.1.7.6)
-      activejob (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    actionmailer (6.1.7.7)
+      actionpack (= 6.1.7.7)
+      actionview (= 6.1.7.7)
+      activejob (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (6.1.7.6)
-      actionview (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    actionpack (6.1.7.7)
+      actionview (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       rack (~> 2.0, >= 2.0.9)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (6.1.7.6)
-      actionpack (= 6.1.7.6)
-      activerecord (= 6.1.7.6)
-      activestorage (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    actiontext (6.1.7.7)
+      actionpack (= 6.1.7.7)
+      activerecord (= 6.1.7.7)
+      activestorage (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       nokogiri (>= 1.8.5)
-    actionview (6.1.7.6)
-      activesupport (= 6.1.7.6)
+    actionview (6.1.7.7)
+      activesupport (= 6.1.7.7)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
@@ -94,14 +94,14 @@ GEM
       activemodel (>= 4.1, < 7.1)
       case_transform (>= 0.2)
       jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
-    activejob (6.1.7.6)
-      activesupport (= 6.1.7.6)
+    activejob (6.1.7.7)
+      activesupport (= 6.1.7.7)
       globalid (>= 0.3.6)
-    activemodel (6.1.7.6)
-      activesupport (= 6.1.7.6)
-    activerecord (6.1.7.6)
-      activemodel (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    activemodel (6.1.7.7)
+      activesupport (= 6.1.7.7)
+    activerecord (6.1.7.7)
+      activemodel (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
     activerecord-import (1.3.0)
       activerecord (>= 4.2)
     activerecord-session_store (2.0.0)
@@ -110,14 +110,14 @@ GEM
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 2.0.8, < 3)
       railties (>= 5.2.4.1)
-    activestorage (6.1.7.6)
-      actionpack (= 6.1.7.6)
-      activejob (= 6.1.7.6)
-      activerecord (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    activestorage (6.1.7.7)
+      actionpack (= 6.1.7.7)
+      activejob (= 6.1.7.7)
+      activerecord (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (6.1.7.6)
+    activesupport (6.1.7.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -198,7 +198,7 @@ GEM
       execjs
     coffee-script-source (1.12.2)
     commonmarker (0.23.10)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     connection_pool (2.3.0)
     countries (5.2.0)
       unaccent (~> 0.3)
@@ -214,7 +214,7 @@ GEM
       csl (~> 2.0)
     daemons (1.1.9)
     database_cleaner (1.7.0)
-    date (3.3.3)
+    date (3.3.4)
     debug_inspector (1.1.0)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
@@ -480,15 +480,15 @@ GEM
     net-http-digest_auth (1.4.1)
     net-http-persistent (4.0.1)
       connection_pool (~> 2.2)
-    net-imap (0.3.7)
+    net-imap (0.4.10)
       date
       net-protocol
     net-ldap (0.17.1)
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.2.1)
+    net-protocol (0.2.2)
       timeout
-    net-smtp (0.3.3)
+    net-smtp (0.4.0.1)
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.0)
@@ -567,7 +567,7 @@ GEM
       nio4r (~> 2.0)
     pyu-ruby-sasl (0.0.3.3)
     racc (1.7.3)
-    rack (2.2.8)
+    rack (2.2.8.1)
     rack-attack (6.6.0)
       rack (>= 1.0, < 3)
     rack-cors (1.1.1)
@@ -584,20 +584,20 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (6.1.7.6)
-      actioncable (= 6.1.7.6)
-      actionmailbox (= 6.1.7.6)
-      actionmailer (= 6.1.7.6)
-      actionpack (= 6.1.7.6)
-      actiontext (= 6.1.7.6)
-      actionview (= 6.1.7.6)
-      activejob (= 6.1.7.6)
-      activemodel (= 6.1.7.6)
-      activerecord (= 6.1.7.6)
-      activestorage (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    rails (6.1.7.7)
+      actioncable (= 6.1.7.7)
+      actionmailbox (= 6.1.7.7)
+      actionmailer (= 6.1.7.7)
+      actionpack (= 6.1.7.7)
+      actiontext (= 6.1.7.7)
+      actionview (= 6.1.7.7)
+      activejob (= 6.1.7.7)
+      activemodel (= 6.1.7.7)
+      activerecord (= 6.1.7.7)
+      activestorage (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       bundler (>= 1.15.0)
-      railties (= 6.1.7.6)
+      railties (= 6.1.7.7)
       sprockets-rails (>= 2.0.0)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
@@ -625,15 +625,15 @@ GEM
       json
       require_all (~> 3.0)
       ruby-progressbar
-    railties (6.1.7.6)
-      actionpack (= 6.1.7.6)
-      activesupport (= 6.1.7.6)
+    railties (6.1.7.7)
+      actionpack (= 6.1.7.7)
+      activesupport (= 6.1.7.7)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
     rainbow (3.1.1)
     raindrops (0.20.0)
-    rake (13.0.6)
+    rake (13.1.0)
     ransack (2.5.0)
       activerecord (>= 5.2.4)
       activesupport (>= 5.2.4)
@@ -886,11 +886,11 @@ GEM
     terser (1.1.8)
       execjs (>= 0.3.0, < 3)
     test-prof (1.0.7)
-    thor (1.2.2)
+    thor (1.3.1)
     tilt (2.0.10)
     time (0.2.2)
       date
-    timeout (0.4.0)
+    timeout (0.4.1)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     ucf (2.0.2)
@@ -936,7 +936,7 @@ GEM
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.7.0)
+    webrick (1.8.1)
     webrobots (0.1.2)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
@@ -949,9 +949,8 @@ GEM
     yaml_db (0.7.0)
       rails (>= 3.0)
       rake (>= 0.8.7)
-    yard (0.9.27)
-      webrick (~> 1.7.0)
-    zeitwerk (2.6.11)
+    yard (0.9.36)
+    zeitwerk (2.6.13)
     zip-container (4.0.2)
       rubyzip (~> 2.0.0)
 

diff --git a/app/assets/images/avatars/workflow_types/avatar-nextflow.png b/app/assets/images/avatars/workflow_types/avatar-nextflow.png
diff --git a/app/models/git_workflow_wizard.rb b/app/models/git_workflow_wizard.rb
@@ -8,14 +8,14 @@
 class GitWorkflowWizard
   include ActiveModel::Model
 
-  attr_reader :next_step, :workflow_class, :git_repository
+  attr_reader :next_step, :git_repository
 
-  attr_accessor :params, :workflow
+  attr_accessor :params, :workflow, :workflow_class
 
   def run
     if new_version?
       @next_step = :new_git_version
-      workflow_class = workflow.workflow_class
+      self.workflow_class = workflow.workflow_class
       current_version = workflow.git_version
       git_version = workflow.git_versions.build(params.delete(:git_version_attributes))
       unless git_version.remote? # It's a new local version, so just use next_version and finish the wizard
@@ -27,7 +27,7 @@ def run
       end
     else
       @next_step = :new
-      self.workflow = Workflow.new
+      self.workflow = Workflow.new(workflow_class: self.workflow_class)
       current_version = nil
     end
 
@@ -61,7 +61,7 @@ def run
         git_version.abstract_cwl_path ||= crate.main_workflow&.cwl_description&.id if crate.main_workflow&.cwl_description&.id
         git_version.diagram_path ||= crate.main_workflow&.diagram&.id if crate.main_workflow&.diagram&.id
 
-        workflow_class ||= WorkflowClass.match_from_metadata(crate&.main_workflow&.programming_language&.properties || {})
+        self.workflow_class ||= WorkflowClass.match_from_metadata(crate&.main_workflow&.programming_language&.properties || {})
       end
     end
 

diff --git a/app/views/assays/_buttons.html.erb b/app/views/assays/_buttons.html.erb
@@ -28,12 +28,12 @@
 
 <% if Seek::Config.project_single_page_enabled %>
 	<% if !displaying_single_page? %>
-		<span>
-     <%= button_link_to("Single Page", 'sop', single_page_path(id: item.projects.first.id, item_type: 'assay', item_id: item.id)) -%>
+		<span title="<%= t("info_text.single_page") %>">
+     <%= button_link_to(t('single_page'), 'sop', single_page_path(id: item.projects.first.id, item_type: 'assay', item_id: item.id)) -%>
     </span>
 	<% else %>
-		<span>
-      <%= button_link_to("Default View", 'sop', assay_path(item.id)) -%>
+		<span title="<%= t('info_text.default_view') %>">
+      <%= button_link_to(t('default_view'), 'sop', assay_path(item.id)) -%>
     </span>
 	<% end %>
 <% end -%>

diff --git a/app/views/assays/show.html.erb b/app/views/assays/show.html.erb
@@ -165,14 +165,18 @@
 	<% if Seek::Config.isa_json_compliance_enabled && @assay.is_isa_json_compliant? %>
 		<%= tab_pane('assay_design') do %>
 			<%= render :partial=>"isa_assays/assay_design", locals: { assay: @assay} -%>
+      <%= render partial: 'single_pages/change_batch_persmission_modal' %>
+      <%= render partial: 'single_pages/upload_excel_modal' %>
 		<% end %>
 	<% end %>
 </div>
 <script>
-  const isIsaCompliant = <%= @assay.is_isa_json_compliant? %>
-  if (isIsaCompliant) {
-    var id = <%= @assay.id %>;
-    var pid = <%= @assay.projects.first.id %>;
-    var dynamicTableDataPath = '<%= Seek::Util.routes.dynamic_table_data_single_page_path(@assay.projects.first.id) %>';
-  }
+    const projectDefaultPolicy = '<%= @assay.projects.first.default_policy_id %>';
+    const isIsaCompliant =
+    <%= @assay.is_isa_json_compliant? %>
+    if (isIsaCompliant) {
+        var id = <%= @assay.id %>;
+        var pid = <%= @assay.projects.first.id %>;
+        var dynamicTableDataPath = '<%= Seek::Util.routes.dynamic_table_data_single_page_path(@assay.projects.first.id) %>';
+    }
 </script>
diff --git a/app/views/investigations/_buttons.html.erb b/app/views/investigations/_buttons.html.erb
@@ -2,12 +2,12 @@
 
 <% if Seek::Config.project_single_page_enabled %>
 	<% if !displaying_single_page? %>
-		<span>
-      <%= button_link_to("Single Page", 'sop', single_page_path(id: item.projects.first.id, item_type: 'investigation', item_id: item.id)) -%>
+		<span title="<%= t("info_text.single_page") %>">
+      <%= button_link_to(t('single_page'), 'sop', single_page_path(id: item.projects.first.id, item_type: 'investigation', item_id: item.id)) -%>
     </span>
 	<% else %>
-		<span>
-      <%= button_link_to("Default View", 'sop', investigation_path(item.id)) -%>
+		<span title="<%= t('info_text.default_view') %>">
+      <%= button_link_to(t('default_view'), 'sop', investigation_path(item.id)) -%>
     </span>
 	<% end %>
 <% end -%>

diff --git a/app/views/projects/_buttons.html.erb b/app/views/projects/_buttons.html.erb
@@ -1,11 +1,11 @@
 <% if Seek::Config.project_single_page_enabled %>
   <% if !displaying_single_page? %>
-    <span>
-      <%= button_link_to("Single Page", 'sop', single_page_path(item.id)) -%>
+    <span title="<%= t("info_text.single_page") %>">
+      <%= button_link_to(t("single_page"), 'sop', single_page_path(item.id)) -%>
     </span>
   <% else %>
-    <span>
-      <%= button_link_to("Default View", 'sop', project_path(item.id)) -%>
+    <span title="<%= t('info_text.default_view') %>">
+      <%= button_link_to(t('default_view'), 'sop', project_path(item.id)) -%>
     </span>
   <% end %>
 <% end -%>

diff --git a/app/views/single_pages/_change_batch_persmission_modal.html.erb b/app/views/single_pages/_change_batch_persmission_modal.html.erb
@@ -0,0 +1,8 @@
+<%= modal(id: 'change-batch-permission-modal', size: 'xl') do %>
+  <%= modal_header("Batch permission changes") %>
+  <%= modal_body do %>
+    <div id="change-batch-permission">
+      hello
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/_upload_excel_modal.html.erb b/app/views/single_pages/_upload_excel_modal.html.erb
@@ -0,0 +1,6 @@
+<%= modal(id: 'upload-excel-modal', size: 'xl') do %>
+  <%= modal_header("Upload from spreadsheet") %>
+  <%= modal_body do %>
+    <div id="upload-excel">...</div>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/show.html.erb b/app/views/single_pages/show.html.erb
@@ -47,22 +47,8 @@
 
     <div id="provide-metadata-content"></div>
 
-    <%= modal(id: 'change-batch-permission-modal', size: 'xl') do %>
-      <%= modal_header("Batch permission changes") %>
-      <%= modal_body do %>
-        <div id="change-batch-permission">
-          hello
-        </div>
-      <% end %>
-    <% end %>
-
-    <%= modal(id: 'upload-excel-modal', size: 'xl') do %>
-      <%= modal_header("Upload from spreadsheet") %>
-      <%= modal_body do %>
-        <div id="upload-excel">...</div>
-      <% end %>
-    <% end %>
-
+  <%= render partial: 'change_batch_persmission_modal' %>
+  <%= render partial: 'upload_excel_modal' %>
 </div>
 
 <script type="text/javascript">