From 47c9b9941418ac8f8ae5ef092269ca45fd10b0f1 Mon Sep 17 00:00:00 2001
From: Adam Coffman <acc@fastmail.com>
Date: Tue, 28 Jan 2025 12:14:50 -0600
Subject: [PATCH] add new task to flag invalid clinvar ids

---
 .../app/jobs/find_invalid_clinvar_records.rb  | 72 +++++++++++++++++++
 server/config/scheduled_tasks.yml             |  6 ++
 2 files changed, 78 insertions(+)
 create mode 100644 server/app/jobs/find_invalid_clinvar_records.rb

diff --git a/server/app/jobs/find_invalid_clinvar_records.rb b/server/app/jobs/find_invalid_clinvar_records.rb
new file mode 100644
index 000000000..7dd8a6f73
--- /dev/null
+++ b/server/app/jobs/find_invalid_clinvar_records.rb
@@ -0,0 +1,72 @@
+class FindInvalidClinvarRecords < ApplicationJob
+  KNOWN_GOOD_ID = 16609
+
+  def perform
+    #Bail early if this fails. Maybe the site is down or something.
+    check_clinvar_id(KNOWN_GOOD_ID) do |succeeded|
+      if !succeeded
+        raise StandardError.new("ClinVar ID #{KNOWN_GOOD_ID} did not return a 200. Aborting checks.")
+      end
+    end
+
+    Variant.joins(:clinvar_entries).distinct.find_each do |variant|
+      variant.clinvar_entries.each do |clinvar_entry|
+        clinvar_id = clinvar_entry.clinvar_id
+
+        if clinvar_id == 'N/A' || clinvar_id == 'NONE FOUND'
+          next
+        end
+
+        if has_existing_flag?(variant, clinvar_id)
+          next
+        end
+
+        check_clinvar_id(clinvar_id) do |succeeded|
+          if !succeeded
+            flag_variant(variant, clinvar_id)
+          end
+        end
+
+        sleep 0.25
+      end
+    end
+  end
+
+  private
+  def url_for_clinvar_id(id)
+    "https://www.ncbi.nlm.nih.gov/clinvar/variation/#{id}/"
+  end
+
+  def check_clinvar_id(id)
+    url = URI.parse(url_for_clinvar_id(id))
+    response = Net::HTTP.get_response(url)
+    case response.code
+    when "200"
+      yield true
+    else
+      yield false
+    end
+  end
+
+  def has_existing_flag?(variant, clinvar_id)
+    verbiage = flag_verbiage(variant, clinvar_id)
+    variant.flags.where(state: 'open', flagging_user_id: Constants::CIVICBOT_USER_ID)
+      .any? { |f| f.open_activity.note == verbiage }
+  end
+
+  def flag_variant(variant, clinvar_id)
+    verbiage = flag_verbiage(variant, clinvar_id)
+    civicbot_user = User.find(Constants::CIVICBOT_USER_ID)
+
+    Activities::FlagEntity.new(
+      flagging_user: civicbot_user,
+      flaggable: variant,
+      organization_id: nil,
+      note: verbiage
+    ).perform
+  end
+
+  def flag_verbiage(variant, clinvar_id)
+    "This Variant links to a ClinVar ID that is no longer valid: #{clinvar_id}"
+  end
+end
diff --git a/server/config/scheduled_tasks.yml b/server/config/scheduled_tasks.yml
index 3528ca427..4c41a5db2 100644
--- a/server/config/scheduled_tasks.yml
+++ b/server/config/scheduled_tasks.yml
@@ -133,3 +133,9 @@ FindRetractedSources:
   description: Check whether sources have been retracted
   queue: default
   class: FindRetractedSources
+
+FindInvalidClinvarRecords:
+  cron: '0 22 1 * *'
+  description: Find and flag Variants that link to invalid ClinVar Records
+  queue: default
+  class: FindInvalidClinvarRecords