update graph count script to generate file in the reports folder

bin/ncbo_generate_graph_count

@@ -11,14 +11,15 @@ 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_relative '../lib/ncbo_cron/graphs_counts'
 
 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"
+  options[:logfile] = STDOUT
   opts.on( '-l', '--logfile FILE', "Write log to FILE (default is 'bulk_load_mapping.log')" ) do |filename|
     options[:logfile] = filename
   end
@@ -32,9 +33,9 @@ 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"
+  logger.error "Please provide a file to save the results as an argument to --store FILEPATH"
   exit
 end
 
-generator = NcboCron::GraphsCounts.new
-generator.run(logger, options[:savefile])
+NcboCron::GraphsCounts.run
+NcboCron::GraphsCounts.run(logger, options[:savefile])

lib/ncbo_cron/graphs_counts.rb

@@ -3,14 +3,16 @@
 require 'optparse'
 
 module NcboCron
-  module GraphsCounts
+  class GraphsCounts
     SUBMISSION_DATA_GRAPH = 'http://data\.bioontology\.org/ontologies/[^/]+/submissions/\d+'
+    DATA_SAVE = 'reports/graph_counts.json'
 
-    def run(logger, file_path)
+    def run(logger, file_path = nil)
+      file_path ||= "#{LinkedData.settings.repository_folder}/#{DATA_SAVE}"
       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)}
+      @all_subs = @all_ontologies.map{|x| x.latest_submission(status: :any)}.compact
 
       logger.info('Fetch all graphs URIs')
       graphs = graphs_list
@@ -35,21 +37,21 @@ def save_result_in_file(file_path, results)
 
     def zombie_graph?(graph)
       regex = Regexp.new(SUBMISSION_DATA_GRAPH)
-      return false unless regex.match?(url)
+      return false unless regex.match?(graph)
 
       !@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} {
+            GRAPH <#{graph}> {
               ?s ?p ?v
             }}
           eos
       rs = Goo.sparql_query_client.query(query)
       count = 0
-      rs.each do |sol|
+      rs.each_solution do |sol|
         count = sol[:count].object
       end
       count
@@ -63,7 +65,7 @@ def graphs_list
             }}
       eos
       rs = Goo.sparql_query_client.query(query)
-      rs.solutions.map { |x| x[:g].to_s }
+      rs.each_solution.map { |x| x[:g].to_s }
     end
   end
 end