diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb
index fc09cfca8..e487264cc 100644
--- a/app/controllers/projects_controller.rb
+++ b/app/controllers/projects_controller.rb
@@ -350,7 +350,7 @@ class ProjectsController < ApplicationController
   def notifications
     @modules = @project.assigned_modules(current_user).order(due_date: :desc)
     render json: {
-      html: render_to_string(partial: 'notifications')
+      html: render_to_string(partial: 'notifications', formats: :html)
     }
   end
 
diff --git a/app/controllers/repository_rows_controller.rb b/app/controllers/repository_rows_controller.rb
index d0b01d61d..00c8a55c5 100644
--- a/app/controllers/repository_rows_controller.rb
+++ b/app/controllers/repository_rows_controller.rb
@@ -84,6 +84,31 @@ class RepositoryRowsController < ApplicationController
     end
   end
 
+  def show
+    @repository_row = RepositoryRow.find_by(id: params[:id])
+    @my_module = MyModule.find_by(id: params[:my_module_id])
+    return render_404 unless @repository_row
+    return render_404 unless @repository_row.repository_id == params[:repository_id].to_i
+    return render_403 unless can_read_repository?(@repository_row.repository)
+    return render_403 if @my_module && !can_read_my_module?(@my_module)
+
+    if @my_module
+      @my_module_assign_error = if !can_assign_my_module_repository_rows?(@my_module)
+                                  I18n.t('repository_row.modal_info.assign_to_task_error.no_access')
+                                elsif @repository_row.my_modules.where(id: @my_module.id).any?
+                                  I18n.t('repository_row.modal_info.assign_to_task_error.already_assigned')
+                                end
+    end
+
+    @assigned_modules = @repository_row.my_modules.joins(experiment: :project)
+    @viewable_modules = @assigned_modules.viewable_by_user(current_user, current_user.teams)
+    @private_modules = @assigned_modules - @viewable_modules
+
+    render json: {
+      html: render_to_string(partial: 'repositories/repository_row_info_modal', formats: :html)
+    }
+  end
+
   def validate_label_template_columns
     label_template = LabelTemplate.where(team_id: current_team.id).find(params[:label_template_id])
 
diff --git a/app/controllers/team_repositories_controller.rb b/app/controllers/team_repositories_controller.rb
index 3840fbeea..266ddaefe 100644
--- a/app/controllers/team_repositories_controller.rb
+++ b/app/controllers/team_repositories_controller.rb
@@ -6,7 +6,7 @@ class TeamRepositoriesController < ApplicationController
 
   # DELETE :team_id/repositories/:repository_id/team_repositories/:id
   def destroy
-    team_shared_object = @repository.team_shared_objects.find(destory_params[:id])
+    team_shared_object = @repository.team_shared_objects.find(destroy_params[:id])
     ActiveRecord::Base.transaction do
       log_activity(:unshare_inventory, team_shared_object)
       team_shared_object.destroy!
@@ -50,7 +50,7 @@ class TeamRepositoriesController < ApplicationController
     params.permit(:team_id, :repository_id, :target_team_id, :permission_level)
   end
 
-  def destory_params
+  def destroy_params
     params.permit(:team_id, :id)
   end
 
diff --git a/spec/controllers/access_permissions/experiments_controller_spec.rb b/spec/controllers/access_permissions/experiments_controller_spec.rb
index 976f6df4e..af2c59257 100644
--- a/spec/controllers/access_permissions/experiments_controller_spec.rb
+++ b/spec/controllers/access_permissions/experiments_controller_spec.rb
@@ -58,7 +58,7 @@ describe AccessPermissions::ExperimentsController, type: :controller do
       {
         id: experiment.id,
         project_id: project.id,
-        experiment_member: {
+        user_assignment: {
           user_role_id: technician_role.id,
           user_id: viewer_user.id
         }
diff --git a/spec/controllers/access_permissions/my_modules_controller_spec.rb b/spec/controllers/access_permissions/my_modules_controller_spec.rb
index 7d16bcd97..a6be67dea 100644
--- a/spec/controllers/access_permissions/my_modules_controller_spec.rb
+++ b/spec/controllers/access_permissions/my_modules_controller_spec.rb
@@ -61,7 +61,7 @@ describe AccessPermissions::MyModulesController, type: :controller do
         id: my_module.id,
         experiment_id: experiment.id,
         project_id: project.id,
-        my_module_member: {
+        user_assignment: {
           user_role_id: technician_role.id,
           user_id: viewer_user.id
         }
diff --git a/spec/controllers/access_permissions/projects_controller_spec.rb b/spec/controllers/access_permissions/projects_controller_spec.rb
index d7f351ec9..4ef1f36c1 100644
--- a/spec/controllers/access_permissions/projects_controller_spec.rb
+++ b/spec/controllers/access_permissions/projects_controller_spec.rb
@@ -100,7 +100,7 @@ describe AccessPermissions::ProjectsController, type: :controller do
     let(:valid_params) do
       {
         id: project.id,
-        project_member: {
+        user_assignment: {
           user_role_id: technician_role.id,
           user_id: normal_user.id
         }
@@ -127,7 +127,7 @@ describe AccessPermissions::ProjectsController, type: :controller do
     let(:valid_params) do
       {
         id: project.id,
-        access_permissions_new_user_project_form: {
+        access_permissions_new_user_form: {
           resource_members: {
             0 => {
               assign: '1',
@@ -193,8 +193,7 @@ describe AccessPermissions::ProjectsController, type: :controller do
     it 'removes the user project and user assigment record' do
       expect {
         delete :destroy, params: valid_params, format: :json
-      }.to change(UserProject, :count).by(-1).and \
-        change(UserAssignment, :count).by(-1)
+      }.to change(UserAssignment, :count).by(-1)
     end
 
     it 'renders 403 if user does not have manage permissions on project' do
diff --git a/spec/controllers/projects_controller_spec.rb b/spec/controllers/projects_controller_spec.rb
index 01f7ed283..7473b190a 100644
--- a/spec/controllers/projects_controller_spec.rb
+++ b/spec/controllers/projects_controller_spec.rb
@@ -68,8 +68,10 @@ describe ProjectsController, type: :controller do
       let(:action) { put :update, params: params }
       let(:params) do
         { id: projects.first.id,
-          project: { name: projects.first.name, team_id: projects.first.team.id,
-                     visibility: projects.first.visibility } }
+          project: { name: projects.first.name,
+                     team_id: projects.first.team.id,
+                     visibility: projects.first.visibility,
+                     default_public_user_role_id: projects.first.default_public_user_role.id } }
       end
 
       it 'returns redirect response' do
@@ -78,10 +80,10 @@ describe ProjectsController, type: :controller do
         expect(response.media_type).to eq 'text/html'
       end
 
-      it 'calls create activity service (change_project_visibility)' do
+      it 'calls create activity service (project_grant_access_to_all_team_members)' do
         params[:project][:visibility] = 'visible'
         expect(Activities::CreateActivityService).to receive(:call)
-          .with(hash_including(activity_type: :change_project_visibility))
+          .with(hash_including(activity_type: :project_grant_access_to_all_team_members))
         action
       end
 
diff --git a/spec/controllers/protocols_controller_spec.rb b/spec/controllers/protocols_controller_spec.rb
index 25b4e2139..6855541f1 100644
--- a/spec/controllers/protocols_controller_spec.rb
+++ b/spec/controllers/protocols_controller_spec.rb
@@ -5,7 +5,7 @@ require 'rails_helper'
 describe ProtocolsController, type: :controller do
   login_user
 
-  include_context 'reference_project_structure'
+  include_context 'reference_project_structure', { team_role: :owner }
 
   describe 'POST create' do
     let(:action) { post :create, params: params, format: :json }
@@ -78,10 +78,12 @@ describe ProtocolsController, type: :controller do
         protocol: {
           name: 'my_test_protocol',
           description: 'description',
-          authors: 'authors'
+          authors: 'authors',
+          elnVersion: '1.0',
         }
       }
     end
+
     let(:action) { post :import, params: params, format: :json }
 
     it 'calls create activity for importing protocols' do
@@ -98,9 +100,9 @@ describe ProtocolsController, type: :controller do
     end
   end
 
-  describe 'PUT description' do
+  describe 'PATCH description' do
     let(:protocol) do
-      create :protocol, :in_public_repository, team: team, added_by: user
+      create :protocol, :in_repository_draft, team: team, added_by: user
     end
     let(:params) do
       {
@@ -110,8 +112,7 @@ describe ProtocolsController, type: :controller do
         }
       }
     end
-    let(:action) { put :update_description, params: params, format: :json }
-
+    let(:action) { patch :update_description, params: params, format: :json }
     it 'calls create activity for updating description' do
       expect(Activities::CreateActivityService)
         .to(receive(:call)
@@ -126,14 +127,14 @@ describe ProtocolsController, type: :controller do
     end
   end
 
-  describe 'POST update_keywords' do
+  describe 'PATCH update_keywords' do
     let(:protocol) do
-      create :protocol, :in_public_repository, team: team, added_by: user
+      create :protocol, :in_repository_draft, team: team, added_by: user
     end
-    let(:action) { put :update_keywords, params: params, format: :json }
     let(:params) do
       { id: protocol.id, keywords: ['keyword-1', 'keyword-2'] }
     end
+    let(:action) { patch :update_keywords, params: params, format: :json }
 
     it 'calls create activity for updating keywords' do
       expect(Activities::CreateActivityService)
@@ -151,7 +152,7 @@ describe ProtocolsController, type: :controller do
 
   context 'update protocol' do
     let(:protocol_repo) do
-      create :protocol, :in_public_repository, name: ' test protocol',
+      create :protocol, :in_repository_published_original, name: ' test protocol',
                                                team: team,
                                                added_by: user
     end
@@ -165,7 +166,7 @@ describe ProtocolsController, type: :controller do
     let(:params) { { id: protocol.id } }
 
     describe 'POST revert' do
-      let(:action) { put :revert, params: params, format: :json }
+      let(:action) { post :revert, params: params, format: :json }
 
       it 'calls create activity for updating protocol in task from repository' do
         expect(Activities::CreateActivityService)
@@ -184,13 +185,13 @@ describe ProtocolsController, type: :controller do
 
   describe 'POST load_from_repository' do
     let(:protocol_source) do
-      create :protocol, :in_public_repository, team: team, added_by: user
+      create :protocol, :in_repository_published_original, team: team, added_by: user
     end
     let(:protocol) { create :protocol, team: team, added_by: user, my_module: my_module }
-    let(:action) { put :load_from_repository, params: params, format: :json }
     let(:params) do
       { source_id: protocol_source.id, id: protocol.id }
     end
+    let(:action) { post :load_from_repository, params: params, format: :json }
 
     it 'calls create activity for loading protocol to task from repository' do
       expect(Activities::CreateActivityService)
@@ -210,13 +211,14 @@ describe ProtocolsController, type: :controller do
     let(:protocol) do
       create :protocol, my_module: my_module, team: team, added_by: user
     end
-    let(:action) { put :load_from_file, params: params, format: :json }
     let(:params) do
       { id: protocol.id,
         protocol: { name: 'my_test_protocol',
                     description: 'description',
-                    authors: 'authors' } }
+                    authors: 'authors',
+                    elnVersion: '1.1'} }
     end
+    let(:action) { post :load_from_file, params: params, format: :json }
 
     it 'calls create activity for loading protocol to task from file' do
       expect(Activities::CreateActivityService)
diff --git a/spec/controllers/result_tables_controller_spec.rb b/spec/controllers/result_tables_controller_spec.rb
index abfe161d5..3cfa5b923 100644
--- a/spec/controllers/result_tables_controller_spec.rb
+++ b/spec/controllers/result_tables_controller_spec.rb
@@ -16,7 +16,8 @@ describe ResultTablesController, type: :controller do
         result:
           { name: 'result name created',
             table_attributes:
-              { contents: '{\"data\":[[\"a\",\"b\",\"1\",null,null]]}' } } }
+              { contents: '{\"data\":[[\"a\",\"b\",\"1\",null,null]]}',
+                metadata: "{\"cells\":[{\"row\":\"0\",\"col\":\"0\",\"className\":\"\",\"calculated\":\"\"}]}" } } }
     end
 
     it 'calls create activity service' do
diff --git a/spec/controllers/steps_controller_spec.rb b/spec/controllers/steps_controller_spec.rb
index 9a5aae59e..a9157a772 100644
--- a/spec/controllers/steps_controller_spec.rb
+++ b/spec/controllers/steps_controller_spec.rb
@@ -10,7 +10,7 @@ describe StepsController, type: :controller do
   }
 
   let(:protocol_repo) do
-    create :protocol, :in_public_repository, team: team, added_by: user
+    create :protocol, :in_repository_draft, team: team, added_by: user
   end
   let(:step_repo) { create :step, protocol: protocol_repo }
 
diff --git a/spec/controllers/team_repositories_controller_spec.rb b/spec/controllers/team_repositories_controller_spec.rb
index ca256fe15..99a043c7d 100644
--- a/spec/controllers/team_repositories_controller_spec.rb
+++ b/spec/controllers/team_repositories_controller_spec.rb
@@ -12,11 +12,11 @@ describe TeamRepositoriesController, type: :controller do
 
   describe 'DELETE destroy' do
     let(:second_team) { create :team, created_by: user }
-    let(:team_repository) { create :team_repository, :read, team: second_team, repository: repository }
+    let(:team_repository) { create :team_shared_object, :read, team: second_team, shared_object: repository }
 
     context 'when resource can be deleted' do
       let(:action) do
-        delete :destroy, params: { repository_id: repository.id, team_id: team.id, id: team_repository.id }
+        delete :destroy, params: { team_id: team.id, id: team_repository.id }
       end
 
       it 'renders 204' do
diff --git a/spec/factories/settings.rb b/spec/factories/settings.rb
index b3f02d575..37b0012aa 100644
--- a/spec/factories/settings.rb
+++ b/spec/factories/settings.rb
@@ -4,5 +4,15 @@ FactoryBot.define do
   factory :settings do
     type { Faker::Lorem.sentence.split(' ').sample }
     values { { key_of_data: Faker::Lorem.sentence.split(' ').sample } }
+
+    trait :with_load_values_from_env_defined do
+      after(:build) do |application_settings|
+        application_settings.define_singleton_method(:load_values_from_env) do
+          {
+            some_key: Faker::Lorem.sentence.split(' ').sample
+          }
+        end
+      end
+    end
   end
 end
diff --git a/spec/factories/team_shared_objects.rb b/spec/factories/team_shared_objects.rb
index 23cc8ab15..3f94db7cd 100644
--- a/spec/factories/team_shared_objects.rb
+++ b/spec/factories/team_shared_objects.rb
@@ -1,10 +1,7 @@
 # frozen_string_literal: true
 
-# frozen_string_literal: true
-
 FactoryBot.define do
   factory :team_shared_object do
-    repository
     trait :read do
       permission_level { :shared_read }
     end
diff --git a/spec/factories/user_assignments.rb b/spec/factories/user_assignments.rb
index e2024830c..a68c27ee3 100644
--- a/spec/factories/user_assignments.rb
+++ b/spec/factories/user_assignments.rb
@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 FactoryBot.define do
   factory :user_assignment do
   end
diff --git a/spec/factories/user_roles.rb b/spec/factories/user_roles.rb
index 1366c0fa6..5cee11a01 100644
--- a/spec/factories/user_roles.rb
+++ b/spec/factories/user_roles.rb
@@ -2,9 +2,7 @@ FactoryBot.define do
   factory :user_role do
     factory :owner_role do
       name { I18n.t('user_roles.predefined.owner') }
-      permissions { ProjectPermissions.constants.map { |const| ProjectPermissions.const_get(const) } +
-                      ExperimentPermissions.constants.map { |const| ExperimentPermissions.const_get(const) } +
-                      MyModulePermissions.constants.map { |const| MyModulePermissions.const_get(const) } }
+      permissions { PredefinedRoles::OWNER_PERMISSIONS }
       predefined { true }
     end
 
diff --git a/spec/fixtures/files/protocol_importers/normalized_single_protocol.json b/spec/fixtures/files/protocol_importers/normalized_single_protocol.json
index 29b823e1b..53224da46 100644
--- a/spec/fixtures/files/protocol_importers/normalized_single_protocol.json
+++ b/spec/fixtures/files/protocol_importers/normalized_single_protocol.json
@@ -6,9 +6,9 @@
     "published_on": 1516132805,
     "version": 0,
     "source_id": 9451,
-    "name": "CUT\u0026RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers",
+    "name": "CUT&amp;RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers",
     "description": {
-      "body": "\u003cdiv class = \"text-blocks\"\u003e\u003cdiv class = \"text-block\"\u003eCleavage Under Targets and Release Using Nuclease (CUT\u0026RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT\u0026RUN has exceptionally low background levels. CUT\u0026RUN outperforms the most widely used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT\u0026RUN is free of solubility and DNA accessibility artifacts and can be used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT\u0026RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT\u0026RUN requires less than a day at the lab bench.\u003c/div\u003e\u003cdiv class = \"text-block\"\u003eIn summary, CUT\u0026RUN has several advantages over ChIP-seq: (1) The method is performed in situ in non-crosslinked cells and does not require chromatin fragmentation or solubilization; (2) The intrinsically low background allows low sequence depth and identification of low signal genomic features invisible to ChIP; (3) The simple procedure can be completed within a day and is suitable for robotic automation; (4) The method can be used with low cell numbers compared to existing methodologies; (5) A simple spike-in strategy can be used for accurate quantitation of protein-DNA interactions. As such, CUT\u0026RUN represents an attractive replacement for ChIPseq, which is one of the most popular methods in biological research.\u003c/div\u003e\u003c/div\u003e",
+      "body": "<div class = \"text-blocks\"><div class = \"text-block\">Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and can be used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT&RUN requires less than a day at the lab bench.</div><div class = \"text-block\">In summary, CUT&RUN has several advantages over ChIP-seq: (1) The method is performed in situ in non-crosslinked cells and does not require chromatin fragmentation or solubilization; (2) The intrinsically low background allows low sequence depth and identification of low signal genomic features invisible to ChIP; (3) The simple procedure can be completed within a day and is suitable for robotic automation; (4) The method can be used with low cell numbers compared to existing methodologies; (5) A simple spike-in strategy can be used for accurate quantitation of protein-DNA interactions. As such, CUT&RUN represents an attractive replacement for ChIPseq, which is one of the most popular methods in biological research.</div></div>",
       "image": "https://s3.amazonaws.com/pr-journal/rzxfw26.png",
       "extra_content": []
     },
@@ -17,8 +17,22 @@
       {
         "source_id": 601564,
         "name": "Binding cells to beads",
+        "attachments": [
+          {
+            "url": "https://pbs.twimg.com/media/Cwu3zrZWQAA7axs.jpg",
+            "name": "First file"
+          },
+          {
+            "url": "http://something.com/wp-content/uploads/2014/11/14506718045_5b3e71dacd_o.jpg",
+            "name": "Second file"
+          },
+          {
+            "url": "http://something.com/wp-content/uploads/2014/11/14506718045_5b3e71dacd_o.jpg",
+            "name": "14506718045_5b3e71dacd_o.jpg"
+          }
+        ],
         "description": {
-          "body": "\u003cdiv class = \"text-blocks\"\u003e\u003cdiv class = \"text-block\"\u003e\u003cspan style = \":justify;\"\u003eHarvest fresh culture(s) at room temperature and count cells. The same protocol can be used for 100 to 250,000 mammalian cells per sample and/or digestion time point.\u003c/span\u003e\u003c/div\u003e\u003c/div\u003e",
+          "body": "<div class = \"text-blocks\"><div class = \"text-block\"><span style = \":justify;\">Harvest fresh culture(s) at room temperature and count cells. The same protocol can be used for 100 to 250,000 mammalian cells per sample and/or digestion time point.</span></div></div>",
           "components": [
             {
               "type": "amount",
@@ -60,11 +74,11 @@
             },
             {
               "type": "result",
-              "body": "\u003cdiv class = \"text-blocks\"\u003e\u003cdiv class = \"text-block\"\u003eCentrifuge 3 min... This is expected result with HTML.\u003c/div\u003e\u003c/div\u003e"
+              "body": "<div class = \"text-blocks\"><div class = \"text-block\">Centrifuge 3 min... This is expected result with HTML.</div></div>"
             },
             {
               "type": "warning",
-              "body": "\u003cdiv class = \"text-blocks\"\u003e\u003cdiv class = \"text-block\"\u003eCentrifuge 3 min... This is WARNING with HTML.\u003c/div\u003e\u003c/div\u003e",
+              "body": "<div class = \"text-blocks\"><div class = \"text-block\">Centrifuge 3 min... This is WARNING with HTML.</div></div>",
               "details": {
                 "link": "www.warnings.com/be_careful"
               }
@@ -99,34 +113,20 @@
             {
               "type": "note",
               "author": "Frank Jones",
-              "body": "\u003cdiv class = \"text-blocks\"\u003e\u003cdiv class = \"text-block\"\u003eCentrifuge 3 min... This is expected result with HTML.\u003c/div\u003e\u003c/div\u003e"
+              "body": "<div class = \"text-blocks\"><div class = \"text-block\">Centrifuge 3 min... This is expected result with HTML.</div></div>"
             }
           ]
         },
-        "attachments": [
-          {
-            "url": "https://pbs.twimg.com/media/Cwu3zrZWQAA7axs.jpg",
-            "name": "First file"
-          },
-          {
-            "url": "http://something.com/wp-content/uploads/2014/11/14506718045_5b3e71dacd_o.jpg",
-            "name": "Second file"
-          },
-          {
-            "url": "http://something.com/wp-content/uploads/2014/11/14506718045_5b3e71dacd_o.jpg",
-            "name": "14506718045_5b3e71dacd_o.jpg"
-          }
-        ],
         "position": 0
       },
       {
         "source_id": 601565,
         "name": "Binding cells to beads 2",
+        "attachments": [],
         "description": {
-          "body": "\u003cdiv class = \"text-blocks\"\u003e\u003cdiv class = \"text-block\"\u003eCentrifuge 3 min 600 x g at room temperature and withdraw liquid.\u003c/div\u003e\u003c/div\u003e",
+          "body": "<div class = \"text-blocks\"><div class = \"text-block\">Centrifuge 3 min 600 x g at room temperature and withdraw liquid.</div></div>",
           "components": []
         },
-        "attachments": [],
         "position": 1
       }
     ]
diff --git a/spec/jobs/user_assignments/propagate_assignment_job_spec.rb b/spec/jobs/user_assignments/propagate_assignment_job_spec.rb
index eb8da07fd..d700a32af 100644
--- a/spec/jobs/user_assignments/propagate_assignment_job_spec.rb
+++ b/spec/jobs/user_assignments/propagate_assignment_job_spec.rb
@@ -42,7 +42,7 @@ module UserAssignments
         create :user_assignment, assignable: my_module_two, user: user_two, user_role: technician_role, assigned_by: user_one
 
         expect {
-          described_class.perform_now(project, user_two, technician_role, user_one, destroy: true)
+          described_class.perform_now(project, user_two.id, technician_role, user_one, destroy: true)
         }.to change(UserAssignment, :count).by(-4)
       end
 
diff --git a/spec/models/connection_spec.rb b/spec/models/connection_spec.rb
index 7fd9b5ac5..4e8a9296f 100644
--- a/spec/models/connection_spec.rb
+++ b/spec/models/connection_spec.rb
@@ -13,8 +13,14 @@ describe Connection, type: :model do
     expect(subject.class).to eq Connection
   end
 
+  describe 'Database table' do
+    it { should have_db_column :id }
+    it { should have_db_column :input_id }
+    it { should have_db_column :output_id }
+  end
+
   describe 'Relations' do
-    #it { should belong_to(:to).class_name('MyModule') }
-    #it { should belong_to(:from).class_name('MyModule') }
+    it { should belong_to(:to).class_name('MyModule').with_foreign_key('input_id').inverse_of(:inputs) }
+    it { should belong_to(:from).class_name('MyModule').with_foreign_key('output_id').inverse_of(:outputs) }
   end
 end
diff --git a/spec/models/connection_step b/spec/models/connection_step
deleted file mode 100644
index 78eda9935..000000000
--- a/spec/models/connection_step
+++ /dev/null
@@ -1,18 +0,0 @@
-require 'rails_helper'
-
-describe Connection, type: :model do
-  it 'should be of class Connection' do
-    expect(subject.class).to eq Connection
-  end
-
-  describe 'Database table' do
-    it { should have_db_column :id }
-    it { should have_db_column :input_id }
-    it { should have_db_column :output_id }
-  end
-
-  describe 'Relations' do
-    it { should belong_to(:to).class_name('MyModule') }
-    it { should belong_to(:from).class_name('MyModule') }
-  end
-end
diff --git a/spec/models/experiment_member_spec.rb b/spec/models/experiment_member_spec.rb
deleted file mode 100644
index c05bd1391..000000000
--- a/spec/models/experiment_member_spec.rb
+++ /dev/null
@@ -1,53 +0,0 @@
-# frozen_string_literal: true
-
-require 'rails_helper'
-
-describe ExperimentMember, type: :model do
-  # let(:owner_role) { create :owner_role }
-  let!(:user) { create :user }
-  let!(:owner_role) { UserRole.find_by(name: I18n.t('user_roles.predefined.owner')) }
-  let!(:project) { create :project }
-  let!(:user_project) { create :user_project, user: user, project: project }
-  let!(:user_assignment) do
-    create :user_assignment,
-           assignable: project,
-           user: user,
-           user_role: owner_role,
-           assigned_by: user
-  end
-  let!(:experiment) { create :experiment, project: project }
-  let(:normal_user_role) { create :normal_user_role }
-
-  let(:subject) { described_class.new(user, experiment, project) }
-
-  describe '#update' do
-    let!(:experiment_user_assignment) do
-      create :user_assignment,
-             assignable: experiment,
-             user: user,
-             user_role: owner_role,
-             assigned_by: user
-    end
-
-    let!(:valid_params) do
-      {
-        user_id: user.id,
-        user_role_id: normal_user_role.id
-      }
-    end
-
-    let!(:subject) { described_class.new(user, experiment, project, user, experiment_user_assignment) }
-
-    it 'updates the assigment user role' do
-      subject.update(valid_params)
-      expect(experiment_user_assignment.reload.user_role).to eq normal_user_role
-    end
-
-    it 'logs a change_user_role_on_my_module activity' do
-      expect {
-        subject.update(valid_params)
-      }.to change(Activity, :count).by(1)
-      expect(Activity.last.type_of).to eq 'change_user_role_on_experiment'
-    end
-  end
-end
diff --git a/spec/models/my_module_member_spec.rb b/spec/models/my_module_member_spec.rb
deleted file mode 100644
index 7c5a9e58f..000000000
--- a/spec/models/my_module_member_spec.rb
+++ /dev/null
@@ -1,36 +0,0 @@
-# frozen_string_literal: true
-
-require 'rails_helper'
-
-describe MyModuleMember, type: :model do
-  # let(:owner_role) { create :owner_role }
-  let!(:user) { create :user }
-  let!(:owner_role) { UserRole.find_by(name: I18n.t('user_roles.predefined.owner')) }
-  let!(:project) { create :project, created_by: user }
-  let!(:experiment) { create :experiment, project: project, created_by: project.created_by }
-  let!(:my_module) { create :my_module, experiment: experiment, created_by: experiment.created_by }
-  let(:normal_user_role) { create :normal_user_role }
-
-  describe '#update' do
-    let!(:valid_params) do
-      {
-        user_id: user.id,
-        user_role_id: normal_user_role.id
-      }
-    end
-
-    let!(:subject) { described_class.new(user, my_module, experiment, project, user) }
-
-    it 'updates the assigment user role' do
-      subject.update(valid_params)
-      expect(subject.user_assignment.user_role).to eq normal_user_role
-    end
-
-    it 'logs a change_user_role_on_my_module activity' do
-      expect {
-        subject.update(valid_params)
-      }.to change(Activity, :count).by(1)
-      expect(Activity.last.type_of).to eq 'change_user_role_on_my_module'
-    end
-  end
-end
diff --git a/spec/models/project_member_spec.rb b/spec/models/project_member_spec.rb
deleted file mode 100644
index 3c46ca189..000000000
--- a/spec/models/project_member_spec.rb
+++ /dev/null
@@ -1,117 +0,0 @@
-# frozen_string_literal: true
-
-require 'rails_helper'
-
-describe ProjectMember, type: :model do
-  let!(:owner_role) { UserRole.find_by(name: I18n.t('user_roles.predefined.owner')) }
-  let!(:user) { create :user }
-  let!(:project) { create :project, created_by: user }
-  let(:normal_user_role) { create :normal_user_role }
-
-  let(:subject) { described_class.new(user, project, user) }
-
-  describe '#update' do
-    let!(:user_project) { create :user_project, user: user, project: project }
-
-    it 'updates only the user assignment role' do
-      subject.user_role_id = normal_user_role.id
-      subject.update
-      expect(subject.user_assignment.user_role).to eq normal_user_role
-    end
-
-    it 'logs a change_user_role_on_project activity' do
-      subject.user_role_id = normal_user_role.id
-      expect {
-        subject.update
-      }.to change(Activity, :count).by(1)
-      expect(Activity.last.type_of).to eq 'change_user_role_on_project'
-    end
-
-    it 'triggers the UserAssignments::PropagateAssignmentJob job' do
-      subject.user_role_id = normal_user_role.id
-      expect(UserAssignments::PropagateAssignmentJob).to receive(:perform_later).with(
-        project, user.id, normal_user_role, user.id
-      )
-      subject.update
-    end
-  end
-
-  describe '#destroy' do
-    let!(:user_two) { create :user }
-    let!(:user_project_two) { create :user_project, user: user_two, project: project }
-    let!(:user_assignment_two) do
-      create :user_assignment,
-             assignable: project,
-             user: user_two,
-             user_role: owner_role,
-             assigned_by: user
-    end
-    let!(:user_project) { create :user_project, user: user, project: project }
-    let!(:user_assignment) { project.user_assignments.first }
-
-    it 'removes the user_assignment and user_project' do
-      expect {
-        subject.destroy
-      }.to change(UserAssignment, :count).by(-1).and \
-           change(UserProject, :count).by(-1)
-    end
-
-    it 'does not remove the user_assignment and user_project if the user is last owner' do
-      user_assignment_two.update!(user_role: normal_user_role)
-
-      expect {
-        subject.destroy
-      }.to change(UserAssignment, :count).by(0).and \
-           change(UserProject, :count).by(0)
-    end
-
-    it 'logs a unassign_user_from_project activity' do
-      expect {
-        subject.destroy
-      }.to change(Activity, :count).by(1)
-      expect(Activity.last.type_of).to eq 'unassign_user_from_project'
-    end
-
-    it 'triggers the UserAssignments::PropagateAssignmentJob job' do
-      expect(UserAssignments::PropagateAssignmentJob).to receive(:perform_later).with(
-        project, user.id, owner_role, user.id, destroy: true
-      )
-      subject.destroy
-    end
-  end
-
-  describe 'validations' do
-    it 'validates presence or user, project, user_role_id when assign is true' do
-      subject = described_class.new(nil, nil)
-      subject.assign = true
-      subject.valid?
-      expect(subject.errors).to have_key(:project)
-      expect(subject.errors).to have_key(:user)
-      expect(subject.errors).to have_key(:user_role_id)
-    end
-
-    it 'validates user project assignment existence' do
-      subject.assign = true
-      subject.user_assignment.user_role_id = owner_role.id
-      subject.valid?
-      expect(subject.errors).to have_key(:user_role_id)
-    end
-
-    describe 'user_role' do
-      it 'adds an error when user role does not exist' do
-        subject.assign = true
-        subject.user_role_id = 1234
-        subject.valid?
-        expect(subject.errors).to have_key(:user_role_id)
-      end
-
-      it 'does not add an error when role exists' do
-        project.user_assignments.destroy_all
-        subject.assign = true
-        subject.user_role_id = owner_role.id
-        subject.valid?
-        expect(subject.errors).not_to have_key(:user_role_id)
-      end
-    end
-  end
-end
diff --git a/spec/models/protocol_spec.rb b/spec/models/protocol_spec.rb
index da175c8ce..49ffbe44d 100644
--- a/spec/models/protocol_spec.rb
+++ b/spec/models/protocol_spec.rb
@@ -95,44 +95,6 @@ describe Protocol, type: :model do
     end
   end
 
-  describe '.publish(user)' do
-    let(:user) { create :user }
-    let(:team) { create :team, created_by: user }
-    let(:protocol) { create :protocol, :in_public_repository, team: team, added_by: user }
-
-    it 'calls create activity for restoring protocol' do
-      expect(Activities::CreateActivityService)
-        .to(receive(:call)
-              .with(hash_including(activity_type:
-                                     :move_protocol_in_repository)))
-
-      protocol.publish user
-    end
-
-    it 'creats one new activity DB' do
-      expect { protocol.publish(user) }.to change { Activity.count }.by(1)
-    end
-  end
-
-  describe '.make_private(user)' do
-    let(:user) { create :user }
-    let(:team) { create :team, created_by: user }
-    let(:protocol) { create :protocol, :in_public_repository, team: team, added_by: user }
-
-    it 'calls create activity for restoring protocol' do
-      expect(Activities::CreateActivityService)
-        .to(receive(:call)
-              .with(hash_including(activity_type:
-                                     :move_protocol_in_repository)))
-
-      protocol.make_private user
-    end
-
-    it 'creats one new activity DB' do
-      expect { protocol.make_private(user) }.to change { Activity.count }.by(1)
-    end
-  end
-
   describe '.deep_clone_repository' do
     let(:user) { create :user }
     let(:team) { create :team, created_by: user }
diff --git a/spec/models/settings_spec.rb b/spec/models/settings_spec.rb
index 3a932c0ba..d608e3894 100644
--- a/spec/models/settings_spec.rb
+++ b/spec/models/settings_spec.rb
@@ -3,14 +3,20 @@
 require 'rails_helper'
 
 describe Settings, type: :model do
-  let(:settings) { build :settings }
+  let(:settings) { build(:settings) }
+  let(:application_settings) { build(:settings, :with_load_values_from_env_defined) }
+
+  it 'raises not NotImplementedError' do
+    expect { settings.load_values_from_env }.to raise_error(NotImplementedError)
+  end
+
 
   it 'is valid' do
-    expect(settings).to be_valid
+    expect(application_settings).to be_valid
   end
 
   it 'should be of class Settings' do
-    expect(subject.class).to eq Settings
+    expect(application_settings.class).to eq Settings
   end
 
   describe 'Database table' do
diff --git a/spec/models/team_shared_object_spec.rb b/spec/models/team_shared_object_spec.rb
index bd33c089b..f21e903a8 100644
--- a/spec/models/team_shared_object_spec.rb
+++ b/spec/models/team_shared_object_spec.rb
@@ -7,16 +7,19 @@ describe TeamSharedObject, type: :model do
   let(:team) { create :team, created_by: user }
   let(:another_team) { create :team, created_by: user }
   let(:repository) { create :repository, team: team, created_by: user }
-  let(:team_shared_object) { build :team_shared_object, :read, team: another_team, shared_repository: repository }
+  let(:team_shared_object) { create :team_shared_object, :read, team: another_team, shared_object: repository }
 
   it 'is valid' do
     expect(team_shared_object).to be_valid
   end
 
+  it 'should be of class TeamSharedObject' do
+    expect(subject.class).to eq TeamSharedObject
+  end
 
-  describe 'Associations' do
-    it { is_expected.to belong_to(:team) }
-    it { is_expected.to belong_to(:shared_repository) }
-    it { is_expected.to belong_to(:shared_object) }
+  describe 'Relations' do
+    it { should belong_to(:team) }
+    it { should belong_to(:shared_object) }
+    it { should belong_to(:shared_repository).optional }
   end
 end
diff --git a/spec/permissions/controllers/experiments_controller_spec.rb b/spec/permissions/controllers/experiments_controller_spec.rb
index 3a84b872c..ec53040ee 100644
--- a/spec/permissions/controllers/experiments_controller_spec.rb
+++ b/spec/permissions/controllers/experiments_controller_spec.rb
@@ -19,8 +19,20 @@ describe ExperimentsController, type: :controller do
     move: { id: 1 },
     module_archive: { id: 1 },
     fetch_workflow_img: { id: 1 },
-    sidebar: { id: 1 }
-  }, []
+    sidebar: { id: 1 },
+    my_modules: { id: 1 },
+    load_table: { id: 1 },
+    permissions: { id: 1 },
+    assigned_users_to_tasks: { id: 1 },
+    batch_clone_my_modules: { id: 1 },
+    search_tags: { id: 1 },
+    actions_dropdown: { id: 1 },
+    archive_my_modules: { id: 1 },
+    table: { id: 1 },
+    move_modules: { id: 1 },
+    move_modules_modal: { id: 1 },
+    view_type: { id: 1, view_type: 'table' },
+  }, [:set_breadcrumbs_items, :my_modules_view_mode]
 
   login_user
 
@@ -87,13 +99,13 @@ describe ExperimentsController, type: :controller do
 
     it_behaves_like "a controller action with permissions checking", :get, :clone_modal do
       let(:testable) { experiment }
-      let(:permissions) { [ExperimentPermissions::MANAGE] }
+      let(:permissions) { [ExperimentPermissions::READ] }
       let(:action_params) { { id: experiment.id } }
     end
 
     it_behaves_like "a controller action with permissions checking", :post, :clone do
       let(:testable) { experiment }
-      let(:permissions) { [ExperimentPermissions::MANAGE] }
+      let(:permissions) { [ExperimentPermissions::READ] }
       let(:action_params) { { id: experiment.id } }
     end
 
diff --git a/spec/permissions/controllers/my_module_repositories_controller_spec.rb b/spec/permissions/controllers/my_module_repositories_controller_spec.rb
index 9348ca6d4..bf1cb77c2 100644
--- a/spec/permissions/controllers/my_module_repositories_controller_spec.rb
+++ b/spec/permissions/controllers/my_module_repositories_controller_spec.rb
@@ -7,6 +7,7 @@ describe MyModuleRepositoriesController, type: :controller do
 
   it_behaves_like "a controller with authentication", {
     index_dt: { my_module_id: 1, id: 1 },
+    create: { my_module_id: 1, id: 1, my_module_tag: { tag_id: 1, my_module_id: 1 } },
     update: { my_module_id: 1, id: 1 },
     update_repository_records_modal: { my_module_id: 1, id: 1 },
     assign_repository_records_modal: { my_module_id: 1, id: 1 },
diff --git a/spec/permissions/controllers/my_modules_controller_spec.rb b/spec/permissions/controllers/my_modules_controller_spec.rb
index 72515ecc2..e2755e769 100644
--- a/spec/permissions/controllers/my_modules_controller_spec.rb
+++ b/spec/permissions/controllers/my_modules_controller_spec.rb
@@ -16,12 +16,19 @@ describe MyModulesController, type: :controller do
     update_description: { id: 1 },
     update_protocol_description: { id: 1 },
     protocols: { id: 1 },
+    protocol: { id: 1 },
+    update_protocol: { id: 1 },
+    provisioning_status: { id: 1 },
+    actions_dropdown: { id: 1 },
+    new: { id: 1, experiment_id: 1 },
+    create: { id: 1, experiment_id: 1 },
+    permissions: { id: 1 },
     results: { id: 1 },
     archive: { id: 1 },
     restore_group: { id: 1 },
     update_state: { id: 1 },
     canvas_dropdown_menu: { id: 1 }
-  }, []
+  }, [:set_breadcrumbs_items]
 
   login_user
 
diff --git a/spec/permissions/controllers/projects_controller_spec.rb b/spec/permissions/controllers/projects_controller_spec.rb
index 5ccc23676..e41094fe6 100644
--- a/spec/permissions/controllers/projects_controller_spec.rb
+++ b/spec/permissions/controllers/projects_controller_spec.rb
@@ -12,8 +12,10 @@ describe ProjectsController, type: :controller do
     show: { id: 1 },
     experiments_cards: { id: 1 },
     notifications: { id: 1 },
+    permissions: { id: 1 },
+    actions_dropdown: { id: 1 },
     view_type: { id: 1 }
-  }, [:current_folder]
+  }, [:current_folder, :set_breadcrumbs_items, :create_tag]
 
   login_user
 
diff --git a/spec/support/reference_project_structure_context.rb b/spec/support/reference_project_structure_context.rb
index 55cfc0042..4af0c0dc1 100644
--- a/spec/support/reference_project_structure_context.rb
+++ b/spec/support/reference_project_structure_context.rb
@@ -34,10 +34,10 @@ RSpec.shared_context 'reference_project_structure' do |config|
     let!(:team_assignment) { create :user_assignment, user: user, assignable: team, user_role: owner_role }
   end
 
-  let!(:project) { create(:project, team: team, created_by: user) }
-  let!(:projects) { create_list(:project, config[:projects], team: team, created_by: user) } if config[:projects]
+  let!(:project) { create(:project, team: team, created_by: user, default_public_user_role_id: team_assignment.user_role.id) }
+  let!(:projects) { create_list(:project, config[:projects], team: team, created_by: user, default_public_user_role_id: team_assignment.user_role.id) } if config[:projects]
 
-  let!(:experiment) { create :experiment, project: project, created_by: project.created_by} unless config[:skip_experiment]
+  let!(:experiment) { create :experiment, project: project, created_by: project.created_by } unless config[:skip_experiment]
   let!(:experiments) { create_list :experiment, config[:experiments], project: project, created_by: project.created_by } if config[:experiments]
 
   let!(:my_module) { create :my_module, experiment: experiment, created_by: experiment.created_by } unless config[:skip_my_module]
diff --git a/spec/utilities/protocol_importers/protocols_io/v3/api_client_spec.rb b/spec/utilities/protocol_importers/protocols_io/v3/api_client_spec.rb
index 4b1a1b0a7..ea0de2e03 100644
--- a/spec/utilities/protocol_importers/protocols_io/v3/api_client_spec.rb
+++ b/spec/utilities/protocol_importers/protocols_io/v3/api_client_spec.rb
@@ -10,7 +10,7 @@ describe ProtocolImporters::ProtocolsIo::V3::ApiClient do
       URL_PUBLICATIONS = "#{CONSTANTS[:base_uri]}publications"
 
       let(:query_params) do
-        { latest: '50' }
+        { latest: '20' }
       end
 
       let(:stub_protocols) do
diff --git a/spec/utilities/protocol_importers/protocols_io/v3/protocol_normalizer_spec.rb b/spec/utilities/protocol_importers/protocols_io/v3/protocol_normalizer_spec.rb
index 0d4d9e5cf..d1be8792a 100644
--- a/spec/utilities/protocol_importers/protocols_io/v3/protocol_normalizer_spec.rb
+++ b/spec/utilities/protocol_importers/protocols_io/v3/protocol_normalizer_spec.rb
@@ -39,7 +39,7 @@ describe ProtocolImporters::ProtocolsIo::V3::ProtocolNormalizer do
         allow(client_data).to receive_message_chain(:parsed_response)
           .and_return(protocols_io_single_protocol)
 
-        expect(subject.normalize_protocol(client_data).deep_stringify_keys).to be == normalized_protocol
+        expect(subject.normalize_protocol(client_data).deep_stringify_keys).to eq(normalized_protocol)
       end
     end