Merge branch 'main' into release

server/app/lib/link_adaptors/fusion_variant.rb

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

server/app/models/frontend_router.rb

@@ -100,7 +100,7 @@ def query_info
   end
 
   def remove_tag(id_with_tag)
-    match = id_with_tag.upcase.match(/^(AID|GID|FID|VID|EID|SID|MPID)(\d+)$/)
+    match = id_with_tag&.upcase&.match(/^(AID|GID|FID|VID|EID|SID|MPID)(\d+)$/)
     if match
       match.captures
     else

server/app/reports/diseases_without_eids.rb

@@ -0,0 +1,30 @@
+class DiseasesWithoutEids < Report
+  attr_reader :diseases_without_associations
+
+  def self.name
+    "Diseases Without Assertions or EIDs"
+  end
+
+  def self.description
+    "Generate a report of diseases that have no assertions or evidence items associated with them."
+  end
+
+  def setup
+    @diseases_without_associations = Disease
+      .left_joins(:assertions, :evidence_items)
+      .group('diseases.id')
+      .having('COUNT(assertions.id) = 0 AND COUNT(evidence_items.id) = 0')
+      .where(deprecated: false)
+      .distinct
+  end
+
+  def headers
+    ['ID', 'DOID', 'Name']
+  end
+
+  def execute
+    diseases_without_associations.each do |disease|
+      data << [disease.id, disease.doid, disease.name]
+    end
+  end
+end

server/app/reports/duplicate_disease_names.rb

@@ -0,0 +1,37 @@
+class DuplicateDiseaseNames < Report
+  attr_reader :duplicate_name_groups
+
+  def self.name
+    "Duplicate Disease Names"
+  end
+
+  def self.description
+    "Generate a report of diseases with duplicate names."
+  end
+
+  def setup
+    @duplicate_name_groups = Disease
+      .select('name, COUNT(*) as disease_count')
+      .where.not(name: nil)
+      .where(deprecated: false)
+      .group(:name)
+      .having('COUNT(*) > 1')
+      .each_with_object({}) do |disease_group, hash|
+        hash[disease_group.name] = Disease.where(name: disease_group.name, deprecated: false)
+      end
+  end
+
+  def headers
+    ['ID', 'DOID', 'Name', 'Assertion Count', 'EID Count']
+  end
+
+  def execute
+    duplicate_name_groups.each do |name, diseases|
+      diseases.each do |disease|
+        num_assertions = disease.assertions.count
+        num_evidence_items = disease.evidence_items.count
+        data << [disease.id, disease.doid, disease.name, num_assertions, num_evidence_items]
+      end
+    end
+  end
+end

server/app/reports/duplicate_doids.rb

@@ -0,0 +1,37 @@
+class DuplicateDoids < Report
+  attr_reader :duplicate_doid_groups
+
+  def self.name
+    "Duplicate DOIDs"
+  end
+
+  def self.description
+    "Generate a report of diseases with duplicate DOIDs."
+  end
+
+  def setup
+    @duplicate_doid_groups = Disease
+      .select('doid, COUNT(*) as disease_count')
+      .where.not(doid: nil)
+      .where(deprecated: false)
+      .group(:doid)
+      .having('COUNT(*) > 1')
+      .each_with_object({}) do |disease_group, hash|
+        hash[disease_group.doid] = Disease.where(doid: disease_group.doid, deprecated: false)
+      end
+  end
+
+  def headers
+    ['ID', 'DOID', 'Name', 'Assertion Count', 'EID Count']
+  end
+
+  def execute
+    duplicate_doid_groups.each do |doid, diseases|
+      diseases.each do |disease|
+        num_assertions = disease.assertions.count
+        num_evidence_items = disease.evidence_items.count
+        data << [disease.id, disease.doid, disease.name, num_assertions, num_evidence_items]
+      end
+    end
+  end
+end

server/app/reports/reports.rb

@@ -2,6 +2,9 @@ module Reports
   AVAILABLE_REPORTS = [
     OrganizationContributions,
     EidsWithOnsetTerms,
-    DiseasesWithIcdo
+    DiseasesWithIcdo,
+    DuplicateDoids,
+    DuplicateDiseaseNames,
+    DiseasesWithoutEids
   ]
 end