Merge branch 'main' into release

server/app/admin/reports_admin.rb

@@ -1,19 +1,21 @@
 Trestle.admin(:reports) do
   menu do
-    item :reports, icon: "fas fa-file-alt"
+    group :tools do
+      item :reports, icon: "fas fa-file-alt"
+    end
   end
 
   controller do
     def index
-      @reports = Report::AVAILABLE_REPORTS
+      @reports = Reports::AVAILABLE_REPORTS
     end
 
     def show
-      @report = Report::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
+      @report = Reports::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
     end
 
     def generate_report
-      @report = Report::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
+      @report = Reports::AVAILABLE_REPORTS.find { |x| params[:name] == x.name }
       report_params = params.permit(@report.inputs.keys).to_h.symbolize_keys
       #checkbox will come in as 0 or 1
       #cast it to a boolean here so reports dont have to worry about that

server/app/admin/utilities_admin.rb

@@ -1,6 +1,8 @@
 Trestle.admin(:utilities) do
   menu do
-    item :utilities, icon: "fas fa-cogs"
+    group :tools do
+      item :utilities, icon: "fas fa-cogs"
+    end
   end
 
   controller do

server/app/graphql/resolvers/quicksearch.rb

@@ -40,7 +40,7 @@ def resolve(query:, types: nil, highlight_matches: false)
       {
         id: res.id,
         name: format_name(res.name, highlights),
-        result_type: res.class,
+        result_type: res.class.base_class,
         matching_text: format_highlights(highlights)
       }
     end

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

server/app/jobs/set_allele_registry_id_single_variant.rb

@@ -21,6 +21,6 @@ def perform(variant)
         delete_allele_registry_link(old_allele_registry_id)
       end
     end
-    GenerateOpenCravatLink.perform_later(self)
+    GenerateOpenCravatLink.perform_later(variant)
   end
 end

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

server/app/lib/link_adaptors/factor_variant.rb

@@ -0,0 +1,4 @@
+module LinkAdaptors
+  class FactorVariant < Variant
+  end
+end

server/app/lib/link_adaptors/gene_variant.rb

@@ -0,0 +1,4 @@
+module LinkAdaptors
+  class GeneVariant < Variant
+  end
+end

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

server/app/reports/report.rb

@@ -1,7 +1,4 @@
 class Report
-  AVAILABLE_REPORTS = [
-    OrganizationContributions
-  ]
 
   def initialize(params)
     setup(**params)

server/app/reports/reports.rb

@@ -0,0 +1,5 @@
+module Reports
+  AVAILABLE_REPORTS = [
+    OrganizationContributions
+  ]
+end