From ae3df839ab1cb10336ad4812a38fd55f9041045f Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Thu, 25 Apr 2024 09:10:00 -0500
Subject: [PATCH] More bugfixes to the background jobs

---
 server/app/jobs/flag_duplicate_allele_registry_ids.rb | 2 +-
 server/app/lib/importer/disease_ontology_mirror.rb    | 4 ++--
 server/app/lib/importer/sequence_ontology_mirror.rb   | 6 +++---
 server/app/lib/scrapers/human_phenotype_ontology.rb   | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/server/app/jobs/flag_duplicate_allele_registry_ids.rb b/server/app/jobs/flag_duplicate_allele_registry_ids.rb
index 0d5e20c33..6867bd4cd 100644
--- a/server/app/jobs/flag_duplicate_allele_registry_ids.rb
+++ b/server/app/jobs/flag_duplicate_allele_registry_ids.rb
@@ -11,7 +11,7 @@ def perform
       variants = Variant.where(id: ids)
       variants.each do |variant|
         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(
+          Activities::FlagEntity.new(
             flagging_user: civicbot_user,
             flaggable: variant,
             organization_id: nil,
diff --git a/server/app/lib/importer/disease_ontology_mirror.rb b/server/app/lib/importer/disease_ontology_mirror.rb
index ff85c3b57..292fd7fef 100644
--- a/server/app/lib/importer/disease_ontology_mirror.rb
+++ b/server/app/lib/importer/disease_ontology_mirror.rb
@@ -142,8 +142,8 @@ 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.open_activity.note == text && c.open_activity.user_id == 385}.count == 0
-          Activity::FlagEntity.new(
+        if obj.flags.select{|f| f.state == 'open' && f.open_activity.note == text && f.open_activity.user_id == 385}.count == 0
+          Activities::FlagEntity.new(
             flagging_user: civicbot_user,
             flaggable: obj,
             organization_id: nil,
diff --git a/server/app/lib/importer/sequence_ontology_mirror.rb b/server/app/lib/importer/sequence_ontology_mirror.rb
index 3f3edf7cd..d9efecb3a 100644
--- a/server/app/lib/importer/sequence_ontology_mirror.rb
+++ b/server/app/lib/importer/sequence_ontology_mirror.rb
@@ -91,12 +91,12 @@ def process_obsolete_terms
               text += " Replaced by #{term['replaced_by']}."
             end
             obsolete_type.variants.each do |variant|
-              if variant.flags.select{|f| f.state == 'open' && f.comments.select{|c| c.text =~ /obsolete Sequence Ontology term/ && c.user_id == 385}.count > 0}.count == 0
-                Actions::FlagEntity.new(
+              if variant.flags.select{|f| f.state == 'open' && f.open_activity.note =~ /obsolete Sequence Ontology term/ && f.open_activity.user_id == 385}.count == 0
+                Activities::FlagEntity.new(
                   flagging_user: civicbot_user,
                   flaggable: variant,
                   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 c703ce834..507003afb 100644
--- a/server/app/lib/scrapers/human_phenotype_ontology.rb
+++ b/server/app/lib/scrapers/human_phenotype_ontology.rb
@@ -44,7 +44,7 @@ def self.update
                 civicbot_user = User.find(385)
                 (p.evidence_items + p.assertions).each do |obj|
                   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(
+                    Activities::FlagEntity.new(
                       flagging_user: civicbot_user,
                       flaggable: obj,
                       organization_id: nil,