From 72ccf8335e8b60c4447cffccc2843b10ba23a4c1 Mon Sep 17 00:00:00 2001
From: Jennifer Vendetti <vendetti@stanford.edu>
Date: Thu, 11 May 2023 14:53:36 -0700
Subject: [PATCH] Refactor parse_json method

Fixes "TypeError (no implicit conversion of URI::HTTPS into String)" exceptions with Ruby 3.x.
---
 app/controllers/application_controller.rb | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 04f03e28f..488cbda5a 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -1,5 +1,4 @@
 require 'uri'
-require 'open-uri'
 require 'net/http'
 require 'net/https'
 require 'net/ftp'
@@ -29,6 +28,8 @@ class ApplicationController < ActionController::Base
   EXPIRY_RECENT_MAPPINGS = 60 * 60     #  1:00 hours
   EXPIRY_ONTOLOGY_SIMPLIFIED = 60 * 1  #  0:01 minute
 
+  RETRY_LIMIT = 1
+
   $trial_license_initialized = false
 
   if !$EMAIL_EXCEPTIONS.nil? && $EMAIL_EXCEPTIONS == true
@@ -579,22 +580,18 @@ def get_apikey()
   end
 
   def parse_json(uri)
-    uri = URI.parse(uri)
     begin
-      response = open(uri, "Authorization" => "apikey token=#{get_apikey}").read
-    rescue Exception => error
+      response = Net::HTTP.get(URI(uri), { 'Authorization' => "apikey token=#{get_apikey}" })
+    rescue StandardError => e
       @retries ||= 0
-      if @retries < 1  # retry once only
-        @retries += 1
-        retry
-      else
-        raise error
-      end
+      raise e unless @retries < RETRY_LIMIT
+
+      @retries += 1
+      retry
     end
     JSON.parse(response)
   end
 
-
   def get_batch_results(params)
     begin
       response = RestClient.post REST_URI_BATCH, params.to_json, :content_type => :json, :accept => :json, :authorization => "apikey token=#{get_apikey}"