From 25e6c06e23ea7909735f77e60e891a377119b214 Mon Sep 17 00:00:00 2001
From: Syphax <gs_bouazzouni@esi.dz>
Date: Sat, 11 Jan 2025 16:39:24 +0100
Subject: [PATCH] add graph count generation job to ncbo_cron

---
 bin/ncbo_cron                  | 20 ++++++++++++++++++++
 bin/ncbo_generate_graph_count  |  7 +------
 lib/ncbo_cron/config.rb        |  2 ++
 lib/ncbo_cron/graphs_counts.rb |  4 ++--
 4 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/bin/ncbo_cron b/bin/ncbo_cron
index 9073f9a1..9e736448 100755
--- a/bin/ncbo_cron
+++ b/bin/ncbo_cron
@@ -374,6 +374,26 @@ runner.execute do |opts|
       ontology_analytics_options[:scheduler_type] = :cron
       ontology_analytics_options[:cron_schedule] = ontology_analytics_options[:cron_ontology_analytics]
       logger.info "Setting up ontology analytics refresh job with #{ontology_analytics_options[:cron_ontology_analytics]}"; logger.flush
+      ontology_analytics_log_path = File.join(log_path, "#{log_filename_noExt}-graph-count.log")
+      ontology_analytics_logger = Logger.new(ontology_analytics_log_path)
+      NcboCron::Scheduler.scheduled_locking_job(ontology_analytics_options) do
+        logger.info "Starting graphs count refresh"; logger.flush
+        logger.info "Logging graphs count refresh details to #{ontology_analytics_log_path}"; logger.flush
+        t0 = Time.now
+        NcboCron::GraphsCounts.new.run(logger)
+        logger.info "Ontology graphs counts completed in #{Time.now - t0} sec."; logger.flush
+        logger.info "Finished graphs refresh"; logger.flush
+      end
+    end
+  end
+
+  if options[:enable_graph_counts]
+    analytics_thread = Thread.new do
+      ontology_analytics_options = options.dup
+      ontology_analytics_options[:job_name] = "ncbo_cron_graph_counts"
+      ontology_analytics_options[:scheduler_type] = :cron
+      ontology_analytics_options[:cron_schedule] = ontology_analytics_options[:cron_ontology_analytics]
+      logger.info "Setting up ontology analytics refresh job with #{ontology_analytics_options[:cron_ontology_analytics]}"; logger.flush
       ontology_analytics_log_path = File.join(log_path, "#{log_filename_noExt}-ontology-analytics.log")
       ontology_analytics_logger = Logger.new(ontology_analytics_log_path)
       NcboCron::Scheduler.scheduled_locking_job(ontology_analytics_options) do
diff --git a/bin/ncbo_generate_graph_count b/bin/ncbo_generate_graph_count
index 276e62a3..68a2612d 100755
--- a/bin/ncbo_generate_graph_count
+++ b/bin/ncbo_generate_graph_count
@@ -32,10 +32,5 @@ opt_parser.parse!
 
 logger = Logger.new(options[:logfile])
 puts "Processing details are logged to #{options[:logfile]}"
-unless options[:savefile]
-  logger.error "Please provide a file to save the results as an argument to --store FILEPATH"
-  exit
-end
 
-NcboCron::GraphsCounts.run
-NcboCron::GraphsCounts.run(logger, options[:savefile])
+NcboCron::GraphsCounts.new.run(logger, options[:savefile])
diff --git a/lib/ncbo_cron/config.rb b/lib/ncbo_cron/config.rb
index f7e4acad..809f7e43 100644
--- a/lib/ncbo_cron/config.rb
+++ b/lib/ncbo_cron/config.rb
@@ -34,6 +34,8 @@ def config(&block)
     @settings.enable_mapping_counts ||= true
     # enable ontology analytics
     @settings.enable_ontology_analytics ||= true
+    # enable graph count
+    @settings.enable_graphs_counts ||= true
     # enable ontologies report
     @settings.enable_ontologies_report ||= true
     # enable index synchronization
diff --git a/lib/ncbo_cron/graphs_counts.rb b/lib/ncbo_cron/graphs_counts.rb
index 4c0b2880..8b8c0f25 100644
--- a/lib/ncbo_cron/graphs_counts.rb
+++ b/lib/ncbo_cron/graphs_counts.rb
@@ -5,10 +5,10 @@
 module NcboCron
   class GraphsCounts
     SUBMISSION_DATA_GRAPH = 'http://data\.bioontology\.org/ontologies/[^/]+/submissions/\d+'
-    DATA_SAVE = 'reports/graph_counts.json'
+    DATA_SAVE = '../../reports/graph_counts.json'
 
     def run(logger, file_path = nil)
-      file_path ||= "#{LinkedData.settings.repository_folder}/#{DATA_SAVE}"
+      file_path ||= DATA_SAVE
       logger.info('Start generating graphs counts')
       logger.info('Fetch ontologies data graphs')
       @all_ontologies = LinkedData::Models::Ontology.all