From 22aa5e9c2575a317f519fa12d041b6432877249c Mon Sep 17 00:00:00 2001
From: gorsyan <79786004+gorsyan@users.noreply.github.com>
Date: Thu, 21 Dec 2023 21:52:58 +0000
Subject: [PATCH] Fixed the job 404 exception error #666 (#710)

* Fix Exception Handling and Implement Error Page
* Fixed the issues that arose from Code Climate
* Last Fix of routes.rb issues
---
 lib/sequenceserver/job.rb    |  2 +-
 lib/sequenceserver/routes.rb | 19 ++++++++++++++++---
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/lib/sequenceserver/job.rb b/lib/sequenceserver/job.rb
index 9f71500a5..cfca2f8dc 100644
--- a/lib/sequenceserver/job.rb
+++ b/lib/sequenceserver/job.rb
@@ -41,7 +41,7 @@ def serializable_classes
       # Fetches job with the given id.
       def fetch(id)
         job_file = File.join(DOTDIR, id, 'job.yaml')
-        fail NotFound unless File.exist?(job_file)
+        return nil unless File.exist?(job_file)
 
         YAML.safe_load_file(
           job_file,
diff --git a/lib/sequenceserver/routes.rb b/lib/sequenceserver/routes.rb
index d3aed40aa..2e17de041 100644
--- a/lib/sequenceserver/routes.rb
+++ b/lib/sequenceserver/routes.rb
@@ -107,6 +107,7 @@ class Routes < Sinatra::Base
     # an empty body if the job hasn't finished yet.
     get '/:jid.json' do |jid|
       job = Job.fetch(jid)
+      halt 404, { error: 'Job not found' }.to_json if job.nil?
       halt 202 unless job.done?
 
       report = Report.generate(job)
@@ -134,10 +135,12 @@ class Routes < Sinatra::Base
 
     # Returns base HTML. Rest happens client-side: polling for and rendering
     # the results.
-    get '/:jid' do
+    get '/:jid' do |jid|
+      job = Job.fetch(jid)
+      raise NotFound, 'Job not found' if job.nil?
+
       erb :report, layout: true
     end
-
     # @params sequence_ids: whitespace separated list of sequence ids to
     # retrieve
     # @params database_ids: whitespace separated list of database ids to
@@ -167,7 +170,9 @@ class Routes < Sinatra::Base
     # Download BLAST report in various formats.
     get '/download/:jid.:type' do |jid, type|
       job = Job.fetch(jid)
+      halt 404, { error: 'Job not found' }.to_json if job.nil?
       out = BLAST::Formatter.new(job, type)
+      halt 404, { error: 'File not found"' }.to_json unless File.exist?(out.filepath)
       send_file out.filepath, filename: out.filename, type: out.mime
     end
 
@@ -175,6 +180,7 @@ class Routes < Sinatra::Base
       content_type :json
       request_params = JSON.parse(request.body.read)
       job = Job.fetch(request_params['job_id'])
+      halt 404, { error: 'Job not found' }.to_json if job.nil?
 
       unless job.done?
         status 422
@@ -279,7 +285,8 @@ class Routes < Sinatra::Base
 
     # Get the query sequences, selected databases, and advanced params used.
     def update_searchdata_from_job(searchdata)
-      job = Job.fetch(params[:job_id])
+      job = fetch_job(params[:job_id])
+      return { error: 'Job not found' }.to_json if job.nil?
       return if job.imported_xml_file
 
       # Only read job.qfile if we are not going to use Database.retrieve.
@@ -301,5 +308,11 @@ def update_searchdata_from_job(searchdata)
         searchdata[:options][method]['last search'] = [job.advanced]
       end
     end
+
+    private
+
+    def fetch_job(job_id)
+      Job.fetch(job_id)
+    end
   end
 end