From 545e13304ac0cd5620900941e998af6bc52e4639 Mon Sep 17 00:00:00 2001
From: aignatov-bio <aignatov@biosistemika.com>
Date: Mon, 21 Sep 2020 14:09:11 +0200
Subject: [PATCH 1/3] Show smart annotation for archived projects/experiments

---
 app/services/smart_annotations/html_preview.rb    |  9 +++------
 app/services/smart_annotations/permission_eval.rb | 15 +++++++--------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/app/services/smart_annotations/html_preview.rb b/app/services/smart_annotations/html_preview.rb
index 206a18d4e..34e1f3df0 100644
--- a/app/services/smart_annotations/html_preview.rb
+++ b/app/services/smart_annotations/html_preview.rb
@@ -13,24 +13,21 @@ module SmartAnnotations
 
       def generate_prj_snippet(_, object)
         if object.archived?
-          return "<a href='#{ROUTES.projects_archive_path}'><span class='sa-type'>Prj</span>" \
-                 "#{object.name}</a>#{I18n.t('atwho.res.archived')}"
+          return "<span class='sa-type'>Prj</span>#{object.name} #{I18n.t('atwho.res.archived')}"
         end
         "<a href='#{ROUTES.project_path(object)}'><span class='sa-type'>Prj</span>#{object.name}</a>"
       end
 
       def generate_exp_snippet(_, object)
         if object.archived?
-          return "<a href='#{ROUTES.experiment_archive_project_path(object.project)}'>" \
-                 "<span class='sa-type'>Exp</span>#{object.name}</a> #{I18n.t('atwho.res.archived')}"
+          return "<span class='sa-type'>Exp</span>#{object.name} #{I18n.t('atwho.res.archived')}"
         end
         "<a href='#{ROUTES.canvas_experiment_path(object)}'><span class='sa-type'>Exp</span>#{object.name}</a>"
       end
 
       def generate_tsk_snippet(_, object)
         if object.archived?
-          return "<a href='#{ROUTES.module_archive_experiment_path(object.experiment
-                 )}'><span class='sa-type'>Tsk</span>#{object.name}</a> #{I18n.t('atwho.res.archived')}"
+          return "<span class='sa-type'>Tsk</span>#{object.name} #{I18n.t('atwho.res.archived')}"
         end
         "<a href='#{ROUTES.protocols_my_module_path(object)}'>" \
         "<span class='sa-type'>Tsk</span>#{object.name}</a>"
diff --git a/app/services/smart_annotations/permission_eval.rb b/app/services/smart_annotations/permission_eval.rb
index e026f93aa..04817a931 100644
--- a/app/services/smart_annotations/permission_eval.rb
+++ b/app/services/smart_annotations/permission_eval.rb
@@ -12,25 +12,24 @@ module SmartAnnotations
       private
 
       def validate_prj_permissions(user, team, object)
-        object.team.id == team.id && can_read_project?(user, object)
+        object.archived = false
+        object.team.id == team.id && can_read_project?(user, object) && object.reload
       end
 
       def validate_exp_permissions(user, team, object)
-        object.project.team.id == team.id && can_read_experiment?(user, object)
+        object.archived = false
+        object.project.team.id == team.id && can_read_experiment?(user, object) && object.reload
       end
 
       def validate_tsk_permissions(user, team, object)
-        object.experiment.project.team.id == team.id &&
-          can_read_experiment?(user, object.experiment)
+        validate_exp_permissions(user, team, object.experiment)
       end
 
       def validate_rep_item_permissions(user, team, object)
-        if object.repository
-          return can_read_repository?(user, object.repository)
-        end
+        return can_read_repository?(user, object.repository) if object.repository
 
         # handles discarded repositories
-        repository = Repository.with_discarded.find_by_id(object.repository_id)
+        repository = Repository.with_discarded.find_by(id: object.repository_id)
         # evaluate to false if repository not found
         return false unless repository
 

From fde33e6e6355fbc3f5f2705f216e888dc1f8e347 Mon Sep 17 00:00:00 2001
From: aignatov-bio <aignatov@biosistemika.com>
Date: Mon, 21 Sep 2020 14:41:51 +0200
Subject: [PATCH 2/3] Fix tests

---
 app/services/smart_annotations/permission_eval.rb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/app/services/smart_annotations/permission_eval.rb b/app/services/smart_annotations/permission_eval.rb
index 04817a931..8d39bc598 100644
--- a/app/services/smart_annotations/permission_eval.rb
+++ b/app/services/smart_annotations/permission_eval.rb
@@ -13,12 +13,16 @@ module SmartAnnotations
 
       def validate_prj_permissions(user, team, object)
         object.archived = false
-        object.team.id == team.id && can_read_project?(user, object) && object.reload
+        permission_check = object.team.id == team.id && can_read_project?(user, object)
+        object.reload
+        permission_check
       end
 
       def validate_exp_permissions(user, team, object)
         object.archived = false
-        object.project.team.id == team.id && can_read_experiment?(user, object) && object.reload
+        permission_check = object.project.team.id == team.id && can_read_experiment?(user, object)
+        object.reload
+        permission_check
       end
 
       def validate_tsk_permissions(user, team, object)

From 653fe6fb1ddf63715f6ce81eef606a945e3071a8 Mon Sep 17 00:00:00 2001
From: aignatov-bio <aignatov@biosistemika.com>
Date: Thu, 24 Sep 2020 11:56:17 +0200
Subject: [PATCH 3/3] Fix markup

---
 app/services/smart_annotations/permission_eval.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/services/smart_annotations/permission_eval.rb b/app/services/smart_annotations/permission_eval.rb
index 8d39bc598..15eb9af60 100644
--- a/app/services/smart_annotations/permission_eval.rb
+++ b/app/services/smart_annotations/permission_eval.rb
@@ -14,14 +14,14 @@ module SmartAnnotations
       def validate_prj_permissions(user, team, object)
         object.archived = false
         permission_check = object.team.id == team.id && can_read_project?(user, object)
-        object.reload
+        object.archived = true if object.archived_changed?
         permission_check
       end
 
       def validate_exp_permissions(user, team, object)
         object.archived = false
         permission_check = object.project.team.id == team.id && can_read_experiment?(user, object)
-        object.reload
+        object.archived = true if object.archived_changed?
         permission_check
       end