Merge pull request #94 from ncbo/develop

Develop -> Master merge, release v6.1.0

Author: alexskr

Gemfile

@@ -20,16 +20,18 @@ gem 'redis'
 gem 'rest-client'
 gem 'sys-proctable'
 
-gem 'net-ftp' # remove in v6.0.0
-
 # Monitoring
 gem 'cube-ruby', require: 'cube'
 
 # NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', tag: 'v5.33.5'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+
+group :development do
+  gem 'rubocop', require: false
+end
 
 group :test do
   gem 'email_spec'

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: b9019ad9e1eb78c74105fc6c6a879085066da17d
-  branch: master
+  revision: c3f9a7f789bf2f52ed31f0272d2725117d3ac04e
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 4fb9114b80b99f0a654c7f70aaa96839c74fc615
-  branch: master
+  revision: 6671099a39fffa8b98f21db7593cef35dd296b65
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -27,8 +27,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: e26859c574c8d9440d8b22eb2388bb1db2f7817a
-  tag: v5.33.5
+  revision: bf575f8dddb28719e8ae64855f9dd9ffc301f046
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -37,6 +37,7 @@ GIT
       json
       libxml-ruby
       multi_json
+      net-ftp
       oj
       omni_logger
       pony
@@ -47,8 +48,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -79,6 +80,7 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
+    ast (2.4.3)
     base64 (0.2.0)
     bcrypt (3.1.20)
     bigdecimal (3.1.9)
@@ -87,7 +89,7 @@ GEM
       logger (~> 1.5)
     coderay (1.1.3)
     concurrent-ruby (1.3.5)
-    connection_pool (2.5.0)
+    connection_pool (2.5.3)
     cube-ruby (0.0.3)
     dante (0.2.0)
     date (3.4.1)
@@ -98,20 +100,20 @@ GEM
       htmlentities (~> 4.3.3)
       launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
-    faraday (2.12.2)
+    faraday (2.13.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
     faraday-follow_redirects (0.3.0)
       faraday (>= 1, < 3)
     faraday-net_http (3.4.0)
       net-http (>= 0.5.0)
-    faraday-retry (2.2.1)
+    faraday-retry (2.3.1)
       faraday (~> 2.0)
-    ffi (1.17.1)
-    ffi (1.17.1-aarch64-linux-gnu)
-    ffi (1.17.1-arm64-darwin)
-    ffi (1.17.1-x86_64-linux-gnu)
+    ffi (1.17.2)
+    ffi (1.17.2-aarch64-linux-gnu)
+    ffi (1.17.2-arm64-darwin)
+    ffi (1.17.2-x86_64-linux-gnu)
     gapic-common (0.25.0)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -192,15 +194,17 @@ GEM
       mutex_m
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.10.2)
+    json (2.11.3)
     json_pure (2.8.1)
     jwt (2.10.1)
       base64
+    language_server-protocol (3.17.0.4)
     launchy (3.1.1)
       addressable (~> 2.8)
       childprocess (~> 5.0)
       logger (~> 1.6)
     libxml-ruby (5.0.3)
+    lint_roller (1.1.0)
     logger (1.7.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -213,7 +217,7 @@ GEM
     mime-types (3.6.2)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2025.0325)
+    mime-types-data (3.2025.0422)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
@@ -226,7 +230,7 @@ GEM
     net-http (0.6.0)
       uri
     net-http-persistent (2.9.4)
-    net-imap (0.5.6)
+    net-imap (0.5.8)
       date
       net-protocol
     net-pop (0.1.2)
@@ -243,23 +247,31 @@ GEM
       logger
     os (1.1.4)
     ostruct (0.6.1)
+    parallel (1.27.0)
     parseconfig (1.1.2)
+    parser (3.3.8.0)
+      ast (~> 2.4.1)
+      racc
     pony (1.13.1)
       mail (>= 2.0)
+    prism (1.4.0)
     pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (6.0.1)
-    rack (3.1.12)
+    racc (1.8.1)
+    rack (3.1.13)
     rack-test (2.2.0)
       rack (>= 1.3)
+    rainbow (3.1.1)
     rake (13.2.1)
     rdf (1.0.8)
       addressable (>= 2.2)
     redis (5.4.0)
       redis-client (>= 0.22.0)
     redis-client (0.24.0)
       connection_pool
+    regexp_parser (2.10.0)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -276,6 +288,21 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
+    rubocop (1.75.4)
+      json (~> 2.3)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
+      parallel (~> 1.10)
+      parser (>= 3.3.0.2)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.44.0, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.44.1)
+      parser (>= 3.3.7.2)
+      prism (~> 1.4)
+    ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     rubyzip (2.4.1)
     rufus-scheduler (2.0.24)
@@ -306,6 +333,9 @@ GEM
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
+    unicode-display_width (3.1.4)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
     uri (1.0.3)
     uuid (2.3.9)
       macaddr (~> 1.0)
@@ -328,7 +358,6 @@ DEPENDENCIES
   multi_json
   ncbo_annotator!
   ncbo_cron!
-  net-ftp
   oj (~> 3.0)
   ontologies_linked_data!
   parseconfig
@@ -337,6 +366,7 @@ DEPENDENCIES
   rake
   redis
   rest-client
+  rubocop
   simplecov
   simplecov-cobertura
   sparql-client!

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2013, The Board of Trustees of Leland Stanford Junior University
+Copyright (c) 2025, The Board of Trustees of Leland Stanford Junior University
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are

README.md

@@ -0,0 +1,17 @@
+# ncbo_cron
+This repository contains scheduled tasks that support the ongoing operations of the 
+[BioPortal](https://bioportal.bioontology.org/) ontology repository.
+
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/ncbo/ncbo_cron/ruby-unit-tests.yml)
+
+## Contact
+Please don't file issues to ask questions. You'll get the fastest response by sending a message to our 
+support list: [[email protected]](mailto:[email protected]).
+
+## Contributors
+<a href="https://github.com/ncbo/ncbo_cron/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=ncbo/ncbo_cron" />
+</a>
+
+## License
+The 2-Clause BSD License. See [LICENSE.txt](/LICENSE.txt) for more information.

bin/ncbo_cron

@@ -66,10 +66,10 @@ opt_parser = OptionParser.new do |opts|
   opts.on("-h", "--redis-host HOST", String, "redis host (for shared locking)", "(default: #{options[:redis_host]})") do |host|
     options[:redis_host] = host
   end
-  opts.on("-p", "--redis-port PORT", Integer, "redis port (for shared locking)", "(default: #{options[:redis_port]})") do |port|
+  opts.on("--redis-port PORT", Integer, "redis port (for shared locking)", "(default: #{options[:redis_port]})") do |port|
     options[:redis_port] = port
   end
-  opts.on("-l", "--log-level LEVEL", String, "set the log level (debug, info, error)", "(default: #{options[:log_level]})") do |c|
+  opts.on("--log-level LEVEL", String, "set the log level (debug, info, error)", "(default: #{options[:log_level]})") do |c|
     options[:log_level] = c.to_sym
   end
   opts.on("-m", "--minutes MIN", Integer, "minutes between process queue checks (override seconds)", "(default: #{options[:minutes_between]})") do |m|
@@ -129,7 +129,7 @@ opt_parser = OptionParser.new do |opts|
   opts.on("-w", "--warm-long-queries SCHED", String, "cron schedule to warmup long time running queries", "(default: #{options[:cron_warmq]})") do |c|
     options[:cron_warmq] = c
   end  
-  opts.on("-m", "--create-mapping-counts SCHED", String, "cron schedule to create mapping counts", "(default: #{options[:cron_mapping_counts]})") do |c|
+  opts.on("--create-mapping-counts SCHED", String, "cron schedule to create mapping counts", "(default: #{options[:cron_mapping_counts]})") do |c|
     options[:cron_mapping_counts] = c
   end
   opts.on("--ontology-analytics SCHED", String, "cron schedule to run ontology analytics refresh", "(default: #{options[:cron_ontology_analytics]})") do |c|
@@ -180,6 +180,13 @@ end
 # Update the NcboCron.settings with CLI options
 options.each_pair {|k,v| NcboCron.settings[k] = v}
 
+# create log dir
+log_dir = File.dirname(options[:log_path])
+begin
+  FileUtils.mkdir_p(log_dir) unless File.directory?(log_dir)
+rescue SystemCallError => e
+  abort "Cannot create log directory #{log_dir}: #{e.message}"
+end
 
 # Configure the process controller
 require 'dante'

lib/ncbo_cron/config.rb

@@ -8,7 +8,6 @@ module NcboCron
   @settings_run = false
   def config(&block)
     return if @settings_run
-    @settings_run = true
 
     # Redis is used for two separate things in ncbo_cron:
     # 1) locating the queue for the submissions to be processed and
@@ -82,17 +81,8 @@ def config(&block)
     @settings.cron_dictionary_generation_cron_job ||= "30 3 * * *"
 
     @settings.log_level ||= :info
-    unless (@settings.log_path && File.exists?(@settings.log_path))
-      log_dir = File.expand_path("../../../logs", __FILE__)
-      FileUtils.mkdir_p(log_dir)
-      @settings.log_path = "#{log_dir}/scheduler.log"
-    end
-    if File.exists?("/var/run/ncbo_cron")
-      pid_path = File.expand_path("/var/run/ncbo_cron/ncbo_cron.pid", __FILE__)
-    else
-      pid_path = File.expand_path("../../../ncbo_cron.pid", __FILE__)
-    end
-    @settings.pid_path ||= pid_path
+    @settings.log_dir  ||= nil          # let caller provide it
+    @settings.log_path ||= nil          # will build it later
 
     # minutes between process queue checks (override seconds)
     @settings.minutes_between ||= 5
@@ -107,5 +97,12 @@ def config(&block)
 
     # Override defaults
     yield @settings if block_given?
+
+    # ── choose defaults *after* user input ───────────────────────────────
+    @settings.log_dir  ||= File.expand_path("log", Dir.pwd)
+    @settings.log_path ||= File.join(@settings.log_dir, "scheduler.log")
+    @settings.pid_path ||= File.expand_path("ncbo_cron.pid", Dir.pwd)
+
+    @settings_run = true
   end
 end