add a script to count graphs in triple store

bin/ncbo_generate_graph_count

@@ -0,0 +1,40 @@
+#!/usr/bin/env ruby
+
+# Exit cleanly from an early interrupt
+Signal.trap("INT") { exit 1 }
+
+# Set up the bundled gems in our environment
+require 'bundler/setup'
+
+# Configure the process for the current cron configuration.
+require_relative '../lib/ncbo_cron'
+config_exists = File.exist?(File.expand_path('../../config/config.rb', __FILE__))
+abort("Please create a config/config.rb file using the config/config.rb.sample as a template") unless config_exists
+require_relative '../config/config'
+
+require 'optparse'
+options = {}
+opt_parser = OptionParser.new do |opts|
+  opts.on('--store FILEPATH', 'save the results in this file') do |filepath|
+    options[:savefile] = filepath
+  end
+  options[:logfile] = "logs/graph_counts_generation.log"
+  opts.on( '-l', '--logfile FILE', "Write log to FILE (default is 'bulk_load_mapping.log')" ) do |filename|
+    options[:logfile] = filename
+  end
+  opts.on( '-h', '--help', 'Display this screen' ) do
+    puts opts
+    exit
+  end
+end
+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"
+  exit
+end
+
+generator = NcboCron::GraphsCounts.new
+generator.run(logger, options[:savefile])

lib/ncbo_cron/graphs_counts.rb

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+require 'logger'
+require 'optparse'
+
+module NcboCron
+  module GraphsCounts
+    SUBMISSION_DATA_GRAPH = 'http://data\.bioontology\.org/ontologies/[^/]+/submissions/\d+'
+
+    def run(logger, file_path)
+      logger.info('Start generating graphs counts')
+      logger.info('Fetch ontologies data graphs')
+      @all_ontologies = LinkedData::Models::Ontology.all
+      @all_subs = all_ontologies.map{|x| x.latest_submission(status: any)}
+
+      logger.info('Fetch all graphs URIs')
+      graphs = graphs_list
+      result = {}
+      graphs.each do |graph|
+        logger.info("Calculate the triple count of #{graph}")
+        result[graph] = [graph_count_triples(graph), zombie_graph?(graph)]
+      end
+
+      logger.info("Save the result in file #{file_path}")
+      save_result_in_file(file_path, result)
+      logger.info('Finish generating graphs counts')
+    end
+
+
+    private
+    def save_result_in_file(file_path, results)
+      File.open(file_path, 'w') do |f|
+        f.write(results.to_json)
+      end
+    end
+
+    def zombie_graph?(graph)
+      regex = Regexp.new(SUBMISSION_DATA_GRAPH)
+      return false unless regex.match?(url)
+
+      !@all_subs.find{ |x| x.id.to_s == graph.to_s }.present?
+    end
+
+    def graph_count_triples(graph)
+      query = <<-eos
+            SELECT (COUNT(?s) as ?count) WHERE {
+            GRAPH #{graph.to_ntriples} {
+              ?s ?p ?v
+            }}
+          eos
+      rs = Goo.sparql_query_client.query(query)
+      count = 0
+      rs.each do |sol|
+        count = sol[:count].object
+      end
+      count
+    end
+
+    def graphs_list
+      query = <<-eos
+            SELECT DISTINCT ?g WHERE {
+            GRAPH ?g {
+              ?s ?p ?v
+            }}
+      eos
+      rs = Goo.sparql_query_client.query(query)
+      rs.solutions.map { |x| x[:g].to_s }
+    end
+  end
+end