From 2fdc2c4f4d197c3797b467fe1f3dd908b77c69ce Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 25 Oct 2023 20:12:04 +0100
Subject: [PATCH 01/16] Adds items that work with setup_new_asset and
 streamlines functionality

---
 app/views/investigations/_form.html.erb       |  9 ---------
 app/views/projects/_project_selector.html.erb | 15 +++++++++++----
 lib/seek/add_buttons.rb                       | 13 ++++++++++++-
 3 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/app/views/investigations/_form.html.erb b/app/views/investigations/_form.html.erb
index 9b13fa8add..0786224709 100644
--- a/app/views/investigations/_form.html.erb
+++ b/app/views/investigations/_form.html.erb
@@ -42,12 +42,3 @@
 
 <%= form_submit_buttons(@investigation) %>
 
-<script>
-    $j(document).ready(function () {   
-        const urlSearchParams = new URLSearchParams(window.location.search);
-        const params = Object.fromEntries(urlSearchParams.entries());
-        const project_id = params["investigation[project_id]"]
-        if(project_id)
-          $j("#projects-selector-select").val(project_id).change();
-    }); 
-</script>
diff --git a/app/views/projects/_project_selector.html.erb b/app/views/projects/_project_selector.html.erb
index b89c0dc3bd..52fd423377 100644
--- a/app/views/projects/_project_selector.html.erb
+++ b/app/views/projects/_project_selector.html.erb
@@ -118,12 +118,19 @@
   });
 
   $j(document).ready(function () {
-      <% if params[:project_ids] && resource && resource.new_record? %>
-      // Auto select projects from params if this is a new object
-      <% params[:project_ids].each do |project_id| %>
-      Sharing.projectsSelector.add(<%= project_id %>, true);
+    // Auto select projects from params[:project_ids] or params[resource][:project_ids] if this is a new object
+    <% if resource && resource.new_record? %>
+      <% if params[:project_ids] %>
+        <% params[:project_ids].each do |project_id| %>
+          Sharing.projectsSelector.add(<%= project_id %>, true);
+        <% end %>
       <% end %>
+      <% if params[controller_name.singularize] && params[controller_name.singularize][:project_ids] %>
+        <% params[controller_name.singularize][:project_ids].each do |project_id| %>
+          Sharing.projectsSelector.add(<%= project_id %>, true);
+        <% end %>
       <% end %>
+    <% end %>
     // Auto select project if there is only one
     if (Sharing.projectsSelector.possibilities.length === 1 &&
         Sharing.projectsSelector.selected.length === 0) {
diff --git a/lib/seek/add_buttons.rb b/lib/seek/add_buttons.rb
index 8b0fe05a25..78aa83eb5b 100644
--- a/lib/seek/add_buttons.rb
+++ b/lib/seek/add_buttons.rb
@@ -2,7 +2,18 @@ module Seek
   # defines what can be added to a particular item, and the params used
   class AddButtons
     DEFINITIONS = {
-      'Project' => [[Investigation, 'investigation[project_id]']],
+      'Project' => [
+        [Investigation, 'investigation[project_ids][]'],
+        [Collection, 'collection[project_ids][]'],
+        [Document, 'document[project_ids][]'],
+        [Event, 'event[project_ids][]'],
+        [FileTemplate, 'file_template[project_ids][]'],
+        [Model, 'model[project_ids][]'],
+        [Placeholder, 'placeholder[project_ids][]'],
+        [Presentation, 'presentation[project_ids][]'],
+        [SampleType, 'sample_type[project_ids][]'],
+        [Sop, 'sop[project_ids][]']
+      ],
       'Investigation' => [[Study, 'study[investigation_id]']],
       'Study' => [[Assay, 'assay[study_id]']],
       'Modelling Analysis' => [[DataFile, 'data_file[assay_assets_attributes[][assay_id]]'],

From 1d3e8dfe94a5cda6a5b2d2d799ce84131196dea8 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 25 Oct 2023 20:13:52 +0100
Subject: [PATCH 02/16] Modifies Publication Strain and Template to work with
 setup_new_asset

---
 app/controllers/publications_controller.rb | 9 ---------
 app/controllers/strains_controller.rb      | 2 +-
 app/controllers/templates_controller.rb    | 2 +-
 lib/seek/add_buttons.rb                    | 5 ++++-
 4 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/app/controllers/publications_controller.rb b/app/controllers/publications_controller.rb
index 4b3ae2a496..75f0a331ae 100644
--- a/app/controllers/publications_controller.rb
+++ b/app/controllers/publications_controller.rb
@@ -56,15 +56,6 @@ def show
     end
   end
 
-  # GET /publications/new
-  def new
-    @publication = Publication.new
-    @publication.parent_name = params[:parent_name]
-    respond_to do |format|
-      format.html # new.html.erb
-    end
-  end
-
   # GET /publications/1/edit
   def edit; end
 
diff --git a/app/controllers/strains_controller.rb b/app/controllers/strains_controller.rb
index 7a3dd2bcd4..9bb6857758 100644
--- a/app/controllers/strains_controller.rb
+++ b/app/controllers/strains_controller.rb
@@ -16,7 +16,7 @@ def new
       @strain = parent_strain.clone_with_associations
       @strain.parent_id = parent_strain.id
     else
-      @strain = Strain.new
+      @strain = setup_new_asset
     end
   end
 
diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
index 9143eef2f3..fcb49a8bd0 100644
--- a/app/controllers/templates_controller.rb
+++ b/app/controllers/templates_controller.rb
@@ -29,7 +29,7 @@ def default_templates
 
   def new
     @tab = 'manual'
-    @template = Template.new
+    @template = setup_new_asset
     @template.organism = 'any'
     respond_with(@template)
   end
diff --git a/lib/seek/add_buttons.rb b/lib/seek/add_buttons.rb
index 78aa83eb5b..f59f932e71 100644
--- a/lib/seek/add_buttons.rb
+++ b/lib/seek/add_buttons.rb
@@ -11,8 +11,11 @@ class AddButtons
         [Model, 'model[project_ids][]'],
         [Placeholder, 'placeholder[project_ids][]'],
         [Presentation, 'presentation[project_ids][]'],
+        [Publication, 'publication[project_ids][]'],
         [SampleType, 'sample_type[project_ids][]'],
-        [Sop, 'sop[project_ids][]']
+        [Sop, 'sop[project_ids][]'],
+        [Strain, 'strain[project_ids][]'],
+        [Template, 'template[project_ids][]']
       ],
       'Investigation' => [[Study, 'study[investigation_id]']],
       'Study' => [[Assay, 'assay[study_id]']],

From 38833c9f2dc8876ebcbd56f1b2129ddd79c8cd9e Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 25 Oct 2023 20:15:01 +0100
Subject: [PATCH 03/16] Forwards params to make datafile work

---
 app/helpers/multi_step_wizard_helper.rb | 6 +++++-
 lib/seek/add_buttons.rb                 | 1 +
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/app/helpers/multi_step_wizard_helper.rb b/app/helpers/multi_step_wizard_helper.rb
index 700104185d..2516645933 100644
--- a/app/helpers/multi_step_wizard_helper.rb
+++ b/app/helpers/multi_step_wizard_helper.rb
@@ -46,6 +46,9 @@ def forward_params(key)
       if params[key][:publication_ids]
         html << hidden_field_tag('data_file[publication_ids][]', params[key][:publication_ids])
       end
+      params[key][:project_ids]&.each do |p|
+        html << hidden_field_tag('data_file[project_ids][]', p)
+      end
     end
     html.html_safe
   end
@@ -56,7 +59,8 @@ def extraction_forward_payload_json(resource, key)
       key => {
         assay_assets_attributes: resource.assay_assets.collect(&:assay_id).collect { |id| { assay_id: id.to_s } },
         event_ids: resource.events.collect(&:id),
-        publication_ids: resource.publications.collect(&:id)
+        publication_ids: resource.publications.collect(&:id),
+        project_ids: resource.projects.collect(&:id)
       }
     }
   end
diff --git a/lib/seek/add_buttons.rb b/lib/seek/add_buttons.rb
index f59f932e71..99999228b9 100644
--- a/lib/seek/add_buttons.rb
+++ b/lib/seek/add_buttons.rb
@@ -5,6 +5,7 @@ class AddButtons
       'Project' => [
         [Investigation, 'investigation[project_ids][]'],
         [Collection, 'collection[project_ids][]'],
+        [DataFile, 'data_file[project_ids][]'],
         [Document, 'document[project_ids][]'],
         [Event, 'event[project_ids][]'],
         [FileTemplate, 'file_template[project_ids][]'],

From bdc23de7e85e32359d76aa13d2a1b5e7e4b8a8a8 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 1 Nov 2023 14:37:23 +0000
Subject: [PATCH 04/16] Forwards params to make samples

---
 app/controllers/samples_controller.rb                         | 2 +-
 app/views/sample_types/select.html.erb                        | 2 +-
 app/views/sample_types/select/_filtered_sample_types.html.erb | 2 +-
 lib/seek/add_buttons.rb                                       | 1 +
 4 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 91d53f5645..28a4903906 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -43,7 +43,7 @@ def new
       @sample = Sample.new(sample_type_id: params[:sample_type_id])
       respond_with(@sample)
     else
-      redirect_to select_sample_types_path(act: :create)
+      redirect_to select_sample_types_path(act: :create, project_ids: params[:sample][:project_ids])
     end
   end
 
diff --git a/app/views/sample_types/select.html.erb b/app/views/sample_types/select.html.erb
index 578d222872..5e439b7112 100644
--- a/app/views/sample_types/select.html.erb
+++ b/app/views/sample_types/select.html.erb
@@ -63,7 +63,7 @@
 <script>
   var SampleTypeFilters={
     optionChanged:function() {
-      $j.ajax('<%= filter_for_select_sample_types_path %>', {
+      $j.ajax('<%= filter_for_select_sample_types_path(project_ids: params[:project_ids]) %>', {
             data: SampleTypeFilters.queryData(),
             success: function (html) {
               $j('#selected-sample-types').html(html);
diff --git a/app/views/sample_types/select/_filtered_sample_types.html.erb b/app/views/sample_types/select/_filtered_sample_types.html.erb
index 3d821b9be7..5b669903e8 100644
--- a/app/views/sample_types/select/_filtered_sample_types.html.erb
+++ b/app/views/sample_types/select/_filtered_sample_types.html.erb
@@ -9,7 +9,7 @@
         </div>
         <% if Sample.can_create? %>
           <div class="col-sm-2">
-            <%= link_to "New sample", new_sample_path(:sample_type_id => sample_type.id), class: "btn btn-primary" %>
+            <%= link_to "New sample", new_sample_path(:sample_type_id => sample_type.id, project_ids: params[:project_ids]), class: "btn btn-primary" %>
           </div>
           <div class="col-sm-2">
             <%= link_to "New batch submission", batch_upload_sample_type_path(sample_type), class: "btn btn-primary" %>
diff --git a/lib/seek/add_buttons.rb b/lib/seek/add_buttons.rb
index 99999228b9..1ea75dcf53 100644
--- a/lib/seek/add_buttons.rb
+++ b/lib/seek/add_buttons.rb
@@ -13,6 +13,7 @@ class AddButtons
         [Placeholder, 'placeholder[project_ids][]'],
         [Presentation, 'presentation[project_ids][]'],
         [Publication, 'publication[project_ids][]'],
+        [Sample, 'sample[project_ids][]'], # Does not work, Sample creation is not standard... have to select SampleType first
         [SampleType, 'sample_type[project_ids][]'],
         [Sop, 'sop[project_ids][]'],
         [Strain, 'strain[project_ids][]'],

From 4671c6909a5c0c0024a5a1c3a88bea2a1fe556cf Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 1 Nov 2023 16:14:49 +0000
Subject: [PATCH 05/16] Forwards params to make workflows work

---
 app/helpers/multi_step_wizard_helper.rb          | 2 +-
 app/views/workflows/_legacy_upload_form.html.erb | 2 ++
 app/views/workflows/_upload_form.html.erb        | 3 +++
 app/views/workflows/select_paths.html.erb        | 1 +
 app/views/workflows/select_ref.html.erb          | 1 +
 lib/seek/add_buttons.rb                          | 5 +++--
 6 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/app/helpers/multi_step_wizard_helper.rb b/app/helpers/multi_step_wizard_helper.rb
index 2516645933..cd180a4ddd 100644
--- a/app/helpers/multi_step_wizard_helper.rb
+++ b/app/helpers/multi_step_wizard_helper.rb
@@ -47,7 +47,7 @@ def forward_params(key)
         html << hidden_field_tag('data_file[publication_ids][]', params[key][:publication_ids])
       end
       params[key][:project_ids]&.each do |p|
-        html << hidden_field_tag('data_file[project_ids][]', p)
+        html << hidden_field_tag("#{key}[project_ids][]", p)
       end
     end
     html.html_safe
diff --git a/app/views/workflows/_legacy_upload_form.html.erb b/app/views/workflows/_legacy_upload_form.html.erb
index 8c3f9c8927..c3e932d4d5 100644
--- a/app/views/workflows/_legacy_upload_form.html.erb
+++ b/app/views/workflows/_legacy_upload_form.html.erb
@@ -12,6 +12,7 @@
   <div class="tab-content">
     <div id="new-ro-crate" role="tabpanel" class="tab-pane active">
       <%= form_tag({ action: :create_ro_crate, anchor: 'new-ro-crate' }, multipart: true) do -%>
+        <%= forward_params(:workflow) %>
         <div class="asset_form">
           <%= error_messages_for :workflow -%>
           <%= error_messages_for :crate_builder, header_message: "Could not build Workflow RO-Crate" -%>
@@ -80,6 +81,7 @@
 
     <div id="existing-ro-crate" role="tabpanel" class="tab-pane">
       <%= form_tag({ action: :create_content_blob, anchor: 'existing-ro-crate' }, multipart: true) do -%>
+        <%= forward_params(:workflow) %>
         <div class="asset_form">
           <%= error_messages_for :workflow -%>
           <%= error_messages_for :crate_extractor -%>
diff --git a/app/views/workflows/_upload_form.html.erb b/app/views/workflows/_upload_form.html.erb
index f04f11f4e6..d2fd75a84d 100644
--- a/app/views/workflows/_upload_form.html.erb
+++ b/app/views/workflows/_upload_form.html.erb
@@ -25,6 +25,7 @@
     <div class="tab-content">
       <div id="new-ro-crate" role="tabpanel" class="tab-pane active">
         <%= form_tag({ action: :create_from_files, anchor: 'new-ro-crate' }, multipart: true) do -%>
+          <%= forward_params(:workflow) %>
           <%= error_messages_for :workflow -%>
           <%= error_messages_for :crate_builder, header_message: "Could not build Workflow RO-Crate" -%>
 
@@ -90,6 +91,7 @@
 
       <div id="git-repo" role="tabpanel" class="tab-pane">
         <%= form_tag({ action: :create_from_git, anchor: 'git-repo' }) do -%>
+          <%= forward_params(:workflow) %>
           <%= error_messages_for :workflow -%>
 
           <%= panel do %>
@@ -109,6 +111,7 @@
 
       <div id="existing-ro-crate" role="tabpanel" class="tab-pane">
         <%= form_tag({ action: :create_from_ro_crate, anchor: 'existing-ro-crate' }, multipart: true) do -%>
+          <%= forward_params(:workflow) %>
           <%= error_messages_for :workflow -%>
           <%= error_messages_for :crate_extractor -%>
 
diff --git a/app/views/workflows/select_paths.html.erb b/app/views/workflows/select_paths.html.erb
index 55f00bf486..5185238ca7 100644
--- a/app/views/workflows/select_paths.html.erb
+++ b/app/views/workflows/select_paths.html.erb
@@ -1,6 +1,7 @@
 <h1>New <%= t('workflow') %><%= ' Version' if @workflow.persisted? %></h1>
 
 <%= form_tag(polymorphic_path(@workflow.persisted? ? [:create_version_from_git, @workflow] : [:create_from_git, :workflows])) do %>
+  <%= hidden_field_tag "workflow[project_ids][]",@workflow.project_ids %>
   <%= fields_for('workflow[git_version_attributes]', @workflow.git_version) do |f| %>
     <% if false %>
       <h2>Version Metadata</h2>
diff --git a/app/views/workflows/select_ref.html.erb b/app/views/workflows/select_ref.html.erb
index fdf909b5c3..f4ff1b6f59 100644
--- a/app/views/workflows/select_ref.html.erb
+++ b/app/views/workflows/select_ref.html.erb
@@ -1,6 +1,7 @@
 <h1>Select Target</h1>
 
 <%= form_tag(polymorphic_path(@workflow.persisted? ? [:create_version_from_git, @workflow] : [:create_from_git, :workflows])) do %>
+  <%= hidden_field_tag "workflow[project_ids][]",@workflow.project_ids %>
   <%= hidden_field_tag "workflow[git_version_attributes][git_repository_id]", @workflow.git_version.git_repository.id %>
   <%= render partial: 'git_repositories/ref_form', locals: { name: "workflow[git_version_attributes][ref]",
                                                              git_repository:  @workflow.git_version.git_repository } %>
diff --git a/lib/seek/add_buttons.rb b/lib/seek/add_buttons.rb
index 1ea75dcf53..e791065f82 100644
--- a/lib/seek/add_buttons.rb
+++ b/lib/seek/add_buttons.rb
@@ -13,11 +13,12 @@ class AddButtons
         [Placeholder, 'placeholder[project_ids][]'],
         [Presentation, 'presentation[project_ids][]'],
         [Publication, 'publication[project_ids][]'],
-        [Sample, 'sample[project_ids][]'], # Does not work, Sample creation is not standard... have to select SampleType first
+        [Sample, 'sample[project_ids][]'],
         [SampleType, 'sample_type[project_ids][]'],
         [Sop, 'sop[project_ids][]'],
         [Strain, 'strain[project_ids][]'],
-        [Template, 'template[project_ids][]']
+        [Template, 'template[project_ids][]'],
+        [Workflow, 'workflow[project_ids][]']
       ],
       'Investigation' => [[Study, 'study[investigation_id]']],
       'Study' => [[Assay, 'assay[study_id]']],

From fd3b51388651466022da2f0333780576ad6f98ee Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Fri, 3 Nov 2023 11:30:03 +0000
Subject: [PATCH 06/16] deals with non-existent params[:sample]

---
 app/controllers/samples_controller.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 28a4903906..025d57c790 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -43,7 +43,8 @@ def new
       @sample = Sample.new(sample_type_id: params[:sample_type_id])
       respond_with(@sample)
     else
-      redirect_to select_sample_types_path(act: :create, project_ids: params[:sample][:project_ids])
+      project_ids_param = params[:sample] ? params[:sample][:project_ids] : {}
+      redirect_to select_sample_types_path(act: :create, project_ids: project_ids_param)
     end
   end
 

From ac115d6e95bd34491bf85ae00b391ab179c7a0aa Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Fri, 3 Nov 2023 15:16:16 +0000
Subject: [PATCH 07/16] fixes project not selected when not in current_projects
 for some assets

---
 app/controllers/concerns/legacy/workflow_support.rb | 2 ++
 app/controllers/sample_types_controller.rb          | 3 ++-
 app/controllers/samples_controller.rb               | 2 +-
 app/controllers/workflows_controller.rb             | 2 ++
 4 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/app/controllers/concerns/legacy/workflow_support.rb b/app/controllers/concerns/legacy/workflow_support.rb
index eb3ca901e1..0b3b262798 100644
--- a/app/controllers/concerns/legacy/workflow_support.rb
+++ b/app/controllers/concerns/legacy/workflow_support.rb
@@ -11,6 +11,7 @@ module WorkflowSupport
     def create_ro_crate
       @crate_builder = Legacy::WorkflowCrateBuilder.new(legacy_ro_crate_params)
       @workflow.workflow_class = @crate_builder.workflow_class = WorkflowClass.find_by_id(params[:workflow_class_id])
+      @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
       blob_params = @crate_builder.build
       @content_blob = ContentBlob.new(blob_params)
 
@@ -31,6 +32,7 @@ def create_content_blob
         if handle_upload_data && @workflow.content_blob.save
           @content_blob = @workflow.content_blob
           @workflow = workflow
+          @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
           if extract_metadata(@content_blob)
             format.html { render :provide_metadata }
           else
diff --git a/app/controllers/sample_types_controller.rb b/app/controllers/sample_types_controller.rb
index df1ce85f49..1424d1ad48 100644
--- a/app/controllers/sample_types_controller.rb
+++ b/app/controllers/sample_types_controller.rb
@@ -28,7 +28,8 @@ def show
   def new
     @tab = 'manual'
 
-    @sample_type = SampleType.new
+    attr = params["sample_type"] ? send("sample_type_params") : {}
+    @sample_type = SampleType.new(attr)
     @sample_type.sample_attributes.build(is_title: true, required: true) # Initial attribute
 
     respond_with(@sample_type)
diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 025d57c790..5dfd77bb28 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -40,7 +40,7 @@ def index
 
   def new
     if params[:sample_type_id]
-      @sample = Sample.new(sample_type_id: params[:sample_type_id])
+      @sample = Sample.new(sample_type_id: params[:sample_type_id], project_ids: params[:project_ids])
       respond_with(@sample)
     else
       project_ids_param = params[:sample] ? params[:sample][:project_ids] : {}
diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index 4be79be5eb..69c9d368de 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -106,6 +106,7 @@ def update
   def create_from_ro_crate
     @crate_extractor = WorkflowCrateExtractor.new(ro_crate_extractor_params)
     @workflow = @crate_extractor.build
+    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
 
     respond_to do |format|
       if @crate_extractor.valid?
@@ -121,6 +122,7 @@ def create_from_files
     @crate_builder = WorkflowRepositoryBuilder.new(ro_crate_params)
     @crate_builder.workflow_class = @workflow.workflow_class
     @workflow = @crate_builder.build
+    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
 
     respond_to do |format|
       if @crate_builder.valid?

From dbff5066db01155f4dfea64488f560c86371ee91 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Fri, 3 Nov 2023 15:38:59 +0000
Subject: [PATCH 08/16] Only see the add button if active member of project

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

diff --git a/app/views/projects/_buttons.html.erb b/app/views/projects/_buttons.html.erb
index 56ced2ae6f..4b98a48c06 100644
--- a/app/views/projects/_buttons.html.erb
+++ b/app/views/projects/_buttons.html.erb
@@ -31,7 +31,7 @@
     </span>
 <% end -%>
 
-<% if item.can_edit? -%>
+<% if item.can_edit? && User.current_user.person.current_projects.include?(item) -%>
   <% if displaying_single_page? %>
     <%= button_link_to("Design #{t('investigation')}", 'new', new_investigation_path("investigation[project_id]": item.id, single_page: params[:id])) %>
   <% else -%>

From 596d7e86f259be2895101086b61da3c75fde72ce Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Fri, 3 Nov 2023 16:04:02 +0000
Subject: [PATCH 09/16] fixes no implicit conversion of nil into Array

---
 app/controllers/concerns/legacy/workflow_support.rb | 4 ++--
 app/controllers/workflows_controller.rb             | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/controllers/concerns/legacy/workflow_support.rb b/app/controllers/concerns/legacy/workflow_support.rb
index 0b3b262798..edbef66ce8 100644
--- a/app/controllers/concerns/legacy/workflow_support.rb
+++ b/app/controllers/concerns/legacy/workflow_support.rb
@@ -11,7 +11,7 @@ module WorkflowSupport
     def create_ro_crate
       @crate_builder = Legacy::WorkflowCrateBuilder.new(legacy_ro_crate_params)
       @workflow.workflow_class = @crate_builder.workflow_class = WorkflowClass.find_by_id(params[:workflow_class_id])
-      @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
+      @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
       blob_params = @crate_builder.build
       @content_blob = ContentBlob.new(blob_params)
 
@@ -32,7 +32,7 @@ def create_content_blob
         if handle_upload_data && @workflow.content_blob.save
           @content_blob = @workflow.content_blob
           @workflow = workflow
-          @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
+          @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
           if extract_metadata(@content_blob)
             format.html { render :provide_metadata }
           else
diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index 69c9d368de..4e2d7b3eef 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -106,7 +106,7 @@ def update
   def create_from_ro_crate
     @crate_extractor = WorkflowCrateExtractor.new(ro_crate_extractor_params)
     @workflow = @crate_extractor.build
-    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
+    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
 
     respond_to do |format|
       if @crate_extractor.valid?
@@ -122,7 +122,7 @@ def create_from_files
     @crate_builder = WorkflowRepositoryBuilder.new(ro_crate_params)
     @crate_builder.workflow_class = @workflow.workflow_class
     @workflow = @crate_builder.build
-    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids]
+    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
 
     respond_to do |format|
       if @crate_builder.valid?

From 8fb7bd9222e472c2fd08a327e2da160b612ac9a8 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Fri, 3 Nov 2023 16:54:40 +0000
Subject: [PATCH 10/16] uses has_member? instead of
 current_projects.include?(item)

---
 app/views/projects/_buttons.html.erb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/views/projects/_buttons.html.erb b/app/views/projects/_buttons.html.erb
index 4b98a48c06..565fb20f8b 100644
--- a/app/views/projects/_buttons.html.erb
+++ b/app/views/projects/_buttons.html.erb
@@ -9,11 +9,11 @@
 <% if can_browse_openbis?(item) %>
     <%= button_link_to("Browse openBIS", :openbis_square, openbis_endpoint_path(item.openbis_endpoints.last),{icon_options:{height:'18px'}}) %>
 <% end %>
-<% if item.try(:has_member?,current_user) %>
+<% if item.has_member?(current_user) %>
     <%= button_link_to("Dashboard", 'project_dashboard', dashboard_project_stats_path(item)) %>
 <% end -%>
 <%= button_link_to('Overview', 'graph_nodes', overview_project_path(item)) -%>
-<% if item.try(:has_member?,current_user) || admin_logged_in? -%>
+<% if item.has_member?(current_user) || admin_logged_in? -%>
     <% tooltip_text="This will present you with a short report about the items that have been shared outside of your #{t('project')}" %>
     <%= button_link_to("Asset report", 'report', asset_report_project_path(item), 'data-tooltip' => tooltip(tooltip_text)) -%>
 <% end -%>
@@ -31,7 +31,7 @@
     </span>
 <% end -%>
 
-<% if item.can_edit? && User.current_user.person.current_projects.include?(item) -%>
+<% if item.can_edit? && item.has_member?(current_user) -%>
   <% if displaying_single_page? %>
     <%= button_link_to("Design #{t('investigation')}", 'new', new_investigation_path("investigation[project_id]": item.id, single_page: params[:id])) %>
   <% else -%>

From 7dd24f5e585ff1b04177773d0329a6c6386c83a3 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Thu, 16 Nov 2023 14:44:48 +0000
Subject: [PATCH 11/16] Adds tests for project controller

---
 test/functional/projects_controller_test.rb | 48 +++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb
index ac1b3add72..ec5f1d8d37 100644
--- a/test/functional/projects_controller_test.rb
+++ b/test/functional/projects_controller_test.rb
@@ -3663,6 +3663,54 @@ def test_admin_can_edit
     assert_select 'a.btn[disabled=disabled]', text: 'Request membership', count: 1
   end
 
+  test 'should not show add new button to admin unless active member' do
+    admin = FactoryBot.create(:admin)
+    project = FactoryBot.create(:project)
+    refute project.has_member?(admin)
+    login_as(admin)
+    assert project.can_edit?
+    get :show, params: { id: project.id }
+    assert_response :success
+    assert_select '#buttons' do
+      assert_select 'div[type=button]', text: /Add new/, count: 0
+    end
+  end
+
+  test 'should show list of directly linkable assets in add new button to active members' do
+    person = FactoryBot.create(:person)
+    project = person.projects.first
+    login_as(person)
+    assert project.has_member?(person)
+    assert project.can_edit?
+    get :show, params: { id: project.id }
+    assert_response :success
+    params = { project_ids: [project.id] }
+    directly_linked_types = [
+      Investigation,
+      Collection,
+      DataFile,
+      Document,
+      Event,
+      FileTemplate,
+      Model,
+      Placeholder,
+      Presentation,
+      Publication,
+      Sample,
+      SampleType,
+      Sop,
+      Strain,
+      Template,
+      Workflow,
+    ]
+    assert_select '#buttons' do
+      assert_select 'div[type=button]', text: /Add new/
+      for type in directly_linked_types
+        assert_select 'a[href=?]', Seek::Util.routes.polymorphic_path(type, action: :new, "#{type.name.underscore}": params)
+      end
+    end
+  end
+
   private
 
   def check_project(project)

From e66050c89da969b540eb9d964105fc6adc7c4411 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 22 Nov 2023 10:59:51 +0000
Subject: [PATCH 12/16] Fix unnecessary send and loop

---
 app/controllers/sample_types_controller.rb | 2 +-
 app/helpers/multi_step_wizard_helper.rb    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/controllers/sample_types_controller.rb b/app/controllers/sample_types_controller.rb
index 1424d1ad48..16207ab68e 100644
--- a/app/controllers/sample_types_controller.rb
+++ b/app/controllers/sample_types_controller.rb
@@ -28,7 +28,7 @@ def show
   def new
     @tab = 'manual'
 
-    attr = params["sample_type"] ? send("sample_type_params") : {}
+    attr = params["sample_type"] ? sample_type_params : {}
     @sample_type = SampleType.new(attr)
     @sample_type.sample_attributes.build(is_title: true, required: true) # Initial attribute
 
diff --git a/app/helpers/multi_step_wizard_helper.rb b/app/helpers/multi_step_wizard_helper.rb
index cd180a4ddd..4f6c9ca563 100644
--- a/app/helpers/multi_step_wizard_helper.rb
+++ b/app/helpers/multi_step_wizard_helper.rb
@@ -46,8 +46,8 @@ def forward_params(key)
       if params[key][:publication_ids]
         html << hidden_field_tag('data_file[publication_ids][]', params[key][:publication_ids])
       end
-      params[key][:project_ids]&.each do |p|
-        html << hidden_field_tag("#{key}[project_ids][]", p)
+      if params[key][:project_ids]
+        html << hidden_field_tag("#{key}[project_ids][]", params[key][:project_ids])
       end
     end
     html.html_safe

From 564ebb6cc46c5ca2a9d4d43bc3160a862c52aa63 Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 22 Nov 2023 11:00:55 +0000
Subject: [PATCH 13/16] Rollback deletion of script needed for project
 selection in single page

---
 app/views/investigations/_form.html.erb | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/app/views/investigations/_form.html.erb b/app/views/investigations/_form.html.erb
index 0786224709..7404a104c9 100644
--- a/app/views/investigations/_form.html.erb
+++ b/app/views/investigations/_form.html.erb
@@ -42,3 +42,12 @@
 
 <%= form_submit_buttons(@investigation) %>
 
+<script>
+  $j(document).ready(function () {
+    const urlSearchParams = new URLSearchParams(window.location.search);
+    const params = Object.fromEntries(urlSearchParams.entries());
+    const project_id = params["investigation[project_id]"]
+    if(project_id)
+      $j("#projects-selector-select").val(project_id).change();
+  });
+</script>

From 614e01f14bc648f007a7c4d0857ffc667434044a Mon Sep 17 00:00:00 2001
From: fherreazcue <francisco.herreazcue@gmail.com>
Date: Wed, 22 Nov 2023 12:29:25 +0000
Subject: [PATCH 14/16] Add project_ids to legacy_ro_crate_params

---
 app/controllers/concerns/legacy/workflow_support.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/controllers/concerns/legacy/workflow_support.rb b/app/controllers/concerns/legacy/workflow_support.rb
index edbef66ce8..75ae62025e 100644
--- a/app/controllers/concerns/legacy/workflow_support.rb
+++ b/app/controllers/concerns/legacy/workflow_support.rb
@@ -11,7 +11,6 @@ module WorkflowSupport
     def create_ro_crate
       @crate_builder = Legacy::WorkflowCrateBuilder.new(legacy_ro_crate_params)
       @workflow.workflow_class = @crate_builder.workflow_class = WorkflowClass.find_by_id(params[:workflow_class_id])
-      @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
       blob_params = @crate_builder.build
       @content_blob = ContentBlob.new(blob_params)
 
@@ -32,7 +31,6 @@ def create_content_blob
         if handle_upload_data && @workflow.content_blob.save
           @content_blob = @workflow.content_blob
           @workflow = workflow
-          @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
           if extract_metadata(@content_blob)
             format.html { render :provide_metadata }
           else
@@ -48,9 +46,11 @@ def create_content_blob
     private
 
     def legacy_ro_crate_params
-      params.require(:ro_crate).permit({ workflow: [:data, :data_url, :make_local_copy] },
+      l_params = params.require(:ro_crate).permit({ workflow: [:data, :data_url, :make_local_copy]},
                                        { abstract_cwl: [:data, :data_url, :make_local_copy] },
                                        { diagram: [:data, :data_url, :make_local_copy] })
+      l_params[:workflow][:project_ids] = params.dig(:workflow, :project_ids) || []
+      l_params
     end
 
     def legacy_set_workflow

From 888fdf72f5d3daadc654d9c333089f9c678d5dfd Mon Sep 17 00:00:00 2001
From: Finn Bacall <finn.bacall@manchester.ac.uk>
Date: Tue, 21 Nov 2023 15:10:19 +0000
Subject: [PATCH 15/16] Include `project_ids` in params

---
 app/controllers/workflows_controller.rb   | 7 +++----
 app/models/workflow_repository_builder.rb | 4 ++--
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index 4e2d7b3eef..f5d8600699 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -104,9 +104,8 @@ def update
 
   # Takes a single RO-Crate zip file
   def create_from_ro_crate
-    @crate_extractor = WorkflowCrateExtractor.new(ro_crate_extractor_params)
+    @crate_extractor = WorkflowCrateExtractor.new(ro_crate_extractor_params.merge(params: workflow_params))
     @workflow = @crate_extractor.build
-    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
 
     respond_to do |format|
       if @crate_extractor.valid?
@@ -122,7 +121,6 @@ def create_from_files
     @crate_builder = WorkflowRepositoryBuilder.new(ro_crate_params)
     @crate_builder.workflow_class = @workflow.workflow_class
     @workflow = @crate_builder.build
-    @workflow.project_ids |= params[:workflow] ? params[:workflow][:project_ids] : params[:project_ids] || []
 
     respond_to do |format|
       if @crate_builder.valid?
@@ -372,7 +370,8 @@ def workflow_params
   def ro_crate_params
     params.require(:ro_crate).permit({ main_workflow: [:data, :data_url, :make_local_copy] },
                                      { abstract_cwl: [:data, :data_url, :make_local_copy] },
-                                     { diagram: [:data, :data_url, :make_local_copy] })
+                                     { diagram: [:data, :data_url, :make_local_copy] }).merge(
+      params.fetch(:workflow, {}).permit(project_ids: []))
   end
 
   def ro_crate_extractor_params
diff --git a/app/models/workflow_repository_builder.rb b/app/models/workflow_repository_builder.rb
index a355d9c39e..def75543c8 100644
--- a/app/models/workflow_repository_builder.rb
+++ b/app/models/workflow_repository_builder.rb
@@ -6,14 +6,14 @@
 class WorkflowRepositoryBuilder
   include ActiveModel::Model
 
-  attr_accessor :main_workflow, :abstract_cwl, :diagram, :workflow_class
+  attr_accessor :main_workflow, :abstract_cwl, :diagram, :workflow_class, :project_ids
 
   validates :main_workflow, presence: true
   validate :resolve_remotes
   validate :workflow_data_present
 
   def build
-    @workflow = Workflow.new(workflow_class: workflow_class, is_git_versioned: true)
+    @workflow = Workflow.new(workflow_class: workflow_class, is_git_versioned: true, project_ids: project_ids || [])
 
     if valid?
       gv = @workflow.git_version

From dadfe1c5c6cef961c09086aabea4f613b2a470c5 Mon Sep 17 00:00:00 2001
From: Finn Bacall <finn.bacall@manchester.ac.uk>
Date: Wed, 22 Nov 2023 14:53:02 +0000
Subject: [PATCH 16/16] Handle case where workflow params not provided

---
 app/controllers/workflows_controller.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb
index f5d8600699..1929cf7960 100644
--- a/app/controllers/workflows_controller.rb
+++ b/app/controllers/workflows_controller.rb
@@ -104,7 +104,8 @@ def update
 
   # Takes a single RO-Crate zip file
   def create_from_ro_crate
-    @crate_extractor = WorkflowCrateExtractor.new(ro_crate_extractor_params.merge(params: workflow_params))
+    @crate_extractor = WorkflowCrateExtractor.new(ro_crate_extractor_params.merge(
+      params: params.key?(:workflow) ? workflow_params : {}))
     @workflow = @crate_extractor.build
 
     respond_to do |format|