implemented #19, #31, and #32

Gemfile.lock

@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 722817503b3effe5ea16c2eb5c10d145808fb6d8
+  revision: c5b78b13ef9e5a77034072303ee8336ae4b3097b
   branch: staging
   specs:
     ncbo_annotator (0.0.1)
@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 15859fe491ec2f3790db04739c9939eb8a7cf909
+  revision: ba5f3c41d7d4ea9102fa508e8a0e14cb6d6a6115
   branch: staging
   specs:
     ontologies_linked_data (0.0.1)
@@ -144,7 +144,7 @@ GEM
     hurley (0.2)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.3.0)
+    json (2.3.1)
     json_pure (2.3.0)
     jwt (2.2.1)
     launchy (2.4.3)

bin/ncbo_ontology_analytics_rebuild

@@ -0,0 +1,65 @@
+#!/usr/bin/env ruby
+
+# Exit cleanly from an early interrupt
+Signal.trap("INT") { exit 1 }
+
+# Setup 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'
+
+platform = "local"
+if LinkedData.settings.goo_host.include? "stage"
+  platform = "stage"
+elsif LinkedData.settings.goo_host.include? "prod"
+  platform = "prod"
+end
+puts "Running on #{platform} platform"
+
+require 'uri'
+require 'benchmark'
+require 'optparse'
+
+options = {}
+opt_parser = OptionParser.new do |opts|
+  # Set a banner, displayed at the top of the help screen.
+  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"
+
+  options[:logfile] = STDOUT
+  opts.on( '-l', '--logfile FILE', "Write log to FILE (default is STDOUT)" ) do |filename|
+    options[:logfile] = filename
+  end
+
+  # Display the help screen, all programs are assumed to have this option.
+  opts.on( '-h', '--help', 'Display this screen' ) do
+    puts opts
+    exit
+  end
+end
+
+opt_parser.parse!
+logger = nil
+
+begin
+  logger = Logger.new(options[:logfile])
+  puts "Processing details are logged to #{options[:logfile] == STDOUT ? "STDOUT" : options[:logfile]}"
+  msg = "Rebuilding ontology analytics repository"
+  puts msg
+  logger.info(msg)
+
+  time = Benchmark.realtime do
+    NcboCron::Models::OntologyAnalytics.new(logger).run
+  end
+  msg = "Completed rebuilding ontology analytics repository in #{(time/60).round(1)} minutes."
+  puts msg
+  logger.info(msg)
+rescue Exception => e
+  msg = "Failed rebuilding ontology analytics repository with exception: #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}"
+  logger.error(msg)
+  puts msg
+  exit(1)
+end

bin/ncbo_ontology_rank_rebuild

@@ -0,0 +1,65 @@
+#!/usr/bin/env ruby
+
+# Exit cleanly from an early interrupt
+Signal.trap("INT") { exit 1 }
+
+# Setup 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'
+
+platform = "local"
+if LinkedData.settings.goo_host.include? "stage"
+  platform = "stage"
+elsif LinkedData.settings.goo_host.include? "prod"
+  platform = "prod"
+end
+puts "Running on #{platform} platform"
+
+require 'uri'
+require 'benchmark'
+require 'optparse'
+
+options = {}
+opt_parser = OptionParser.new do |opts|
+  # Set a banner, displayed at the top of the help screen.
+  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"
+
+  options[:logfile] = STDOUT
+  opts.on( '-l', '--logfile FILE', "Write log to FILE (default is STDOUT)" ) do |filename|
+    options[:logfile] = filename
+  end
+
+  # Display the help screen, all programs are assumed to have this option.
+  opts.on( '-h', '--help', 'Display this screen' ) do
+    puts opts
+    exit
+  end
+end
+
+opt_parser.parse!
+logger = nil
+
+begin
+  logger = Logger.new(options[:logfile])
+  puts "Processing details are logged to #{options[:logfile] == STDOUT ? "STDOUT" : options[:logfile]}"
+  msg = "Rebuilding ontology rank repository"
+  puts msg
+  logger.info(msg)
+
+  time = Benchmark.realtime do
+    NcboCron::Models::OntologyRank.new(logger).run
+  end
+  msg = "Completed rebuilding ontology rank repository in #{time.round(1)} seconds."
+  puts msg
+  logger.info(msg)
+rescue Exception => e
+  msg = "Failed rebuilding ontology rank repository with exception: #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}"
+  logger.error(msg)
+  puts msg
+  exit(1)
+end

bin/ncbo_ontology_report_rebuild

@@ -0,0 +1,65 @@
+#!/usr/bin/env ruby
+
+# Exit cleanly from an early interrupt
+Signal.trap("INT") { exit 1 }
+
+# Setup 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'
+
+platform = "local"
+if LinkedData.settings.goo_host.include? "stage"
+  platform = "stage"
+elsif LinkedData.settings.goo_host.include? "prod"
+  platform = "prod"
+end
+puts "Running on #{platform} platform"
+
+require 'uri'
+require 'benchmark'
+require 'optparse'
+
+options = {}
+opt_parser = OptionParser.new do |opts|
+  # Set a banner, displayed at the top of the help screen.
+  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"
+
+  options[:logfile] = STDOUT
+  opts.on( '-l', '--logfile FILE', "Write log to FILE (default is STDOUT)" ) do |filename|
+    options[:logfile] = filename
+  end
+
+  # Display the help screen, all programs are assumed to have this option.
+  opts.on( '-h', '--help', 'Display this screen' ) do
+    puts opts
+    exit
+  end
+end
+
+opt_parser.parse!
+logger = nil
+
+begin
+  logger = Logger.new(options[:logfile])
+  puts "Processing details are logged to #{options[:logfile] == STDOUT ? "STDOUT" : options[:logfile]}"
+  msg = "Rebuilding ontologies report"
+  puts msg
+  logger.info(msg)
+
+  time = Benchmark.realtime do
+    NcboCron::Models::OntologiesReport.new(logger).run
+  end
+  msg = "Completed rebuilding ontologies report in #{(time/60).round(1)} minutes."
+  puts msg
+  logger.info(msg)
+rescue Exception => e
+  msg = "Failed rebuilding ontologies report with exception: #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}"
+  logger.error(msg)
+  puts msg
+  exit(1)
+end

lib/ncbo_cron.rb

@@ -11,6 +11,7 @@
 require_relative 'ncbo_cron/query_caching'
 require_relative 'ncbo_cron/ontologies_report'
 require_relative 'ncbo_cron/ontology_analytics'
+require_relative 'ncbo_cron/ontology_rank'
 require_relative 'ncbo_cron/spam_deletion'
 require_relative 'ncbo_cron/mapping_counts'
 require_relative 'ncbo_cron/update_manager'