From 17ad7058fdf4f86bed2dea9ac055d17151d59e09 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Fri, 19 Apr 2024 14:42:11 -0500
Subject: [PATCH] Background jobs that flag entities should use the activity,
 not the action

---
 server/app/jobs/flag_duplicate_allele_registry_ids.rb | 6 +++---
 server/app/lib/importer/disease_ontology_mirror.rb    | 6 +++---
 server/app/lib/scrapers/human_phenotype_ontology.rb   | 6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/server/app/jobs/flag_duplicate_allele_registry_ids.rb b/server/app/jobs/flag_duplicate_allele_registry_ids.rb
index 6bb7ee5e1..0d5e20c33 100644
--- a/server/app/jobs/flag_duplicate_allele_registry_ids.rb
+++ b/server/app/jobs/flag_duplicate_allele_registry_ids.rb
@@ -10,12 +10,12 @@ def perform
     duplicates.each do |caid, ids|
       variants = Variant.where(id: ids)
       variants.each do |variant|
-        if variant.flags.select{|f| f.state == 'open' && f.comments.select{|c| c.text =~ /This Variant may be a duplicate and may need to be deprecated/ && c.user_id == 385}.count > 0}.count == 0
-          Actions::FlagEntity.new(
+        if variant.flags.select{|f| f.state == 'open' && f.open_activity.note =~ /This Variant may be a duplicate and may need to be deprecated/ && f.open_activity.user_id == 385}.count == 0
+          Activity::FlagEntity.new(
             flagging_user: civicbot_user,
             flaggable: variant,
             organization_id: nil,
-            comment: "The Allele Registry ID of this Variant is used more than once. This Variant may be a duplicate and may need to be deprecated. The following Variants all resolved to Allele Registry ID \"#{caid}\": #{ids.join(', ')}"
+            note: "The Allele Registry ID of this Variant is used more than once. This Variant may be a duplicate and may need to be deprecated. The following Variants all resolved to Allele Registry ID \"#{caid}\": #{ids.join(', ')}"
           ).perform
         end
       end
diff --git a/server/app/lib/importer/disease_ontology_mirror.rb b/server/app/lib/importer/disease_ontology_mirror.rb
index f0f6ee790..ff85c3b57 100644
--- a/server/app/lib/importer/disease_ontology_mirror.rb
+++ b/server/app/lib/importer/disease_ontology_mirror.rb
@@ -142,12 +142,12 @@ def url_from_doid(doid)
     def add_flags(disease, text)
       civicbot_user = User.find(385)
       (disease.evidence_items + disease.assertions).each do |obj|
-        if obj.flags.select{|f| f.state == 'open' && f.comments.select{|c| c.comment == text && c.user_id == 385}.count > 0}.count == 0
-          Actions::FlagEntity.new(
+        if obj.flags.select{|f| f.state == 'open' && f.open_activity.note == text && c.open_activity.user_id == 385}.count == 0
+          Activity::FlagEntity.new(
             flagging_user: civicbot_user,
             flaggable: obj,
             organization_id: nil,
-            comment: text
+            note: text
           ).perform
         end
       end
diff --git a/server/app/lib/scrapers/human_phenotype_ontology.rb b/server/app/lib/scrapers/human_phenotype_ontology.rb
index b68b5ee60..c703ce834 100644
--- a/server/app/lib/scrapers/human_phenotype_ontology.rb
+++ b/server/app/lib/scrapers/human_phenotype_ontology.rb
@@ -43,12 +43,12 @@ def self.update
               else
                 civicbot_user = User.find(385)
                 (p.evidence_items + p.assertions).each do |obj|
-                  if obj.flags.select{|f| f.state == 'open' && f.comments.select{|c| c.text =~ /deprecated HPO term/ && c.user_id == 385}.count > 0}.count == 0
-                    Actions::FlagEntity.new(
+                  if obj.flags.select{|f| f.state == 'open' && f.open_activity.note =~ /deprecated HPO term/ && f.open_activity.user_id == 385}.count == 0
+                    Activity::FlagEntity.new(
                       flagging_user: civicbot_user,
                       flaggable: obj,
                       organization_id: nil,
-                      comment: "This entity uses a deprecated HPO term \"#{name}\" (#{hpo_id})"
+                      note: "This entity uses a deprecated HPO term \"#{name}\" (#{hpo_id})"
                     ).perform
                   end
                 end