bio-ucsc-api 0.6.3 → 0.6.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a77540fb8707f8099fcfbc13d34db96f783c5b13
-  data.tar.gz: 4e2fc3f457369a60a95cb067c4ed4647f5c72496
+  metadata.gz: 311396963dc89a3bf96a30cf27dff0a628904e4e
+  data.tar.gz: fdf5034e668c1180ec84d0a9d496a036063743b4
 SHA512:
-  metadata.gz: 2767a50a940540e43010d0d3e7a76a91e315d76f946ca18b6e2cc080f8e2c3f91435cd78a3cea762eacfdf1c47a14555cbc6d0b68c4f9c6422590ed3041c1153
-  data.tar.gz: b8931cd9a059ffaf89d736900c958926198faaf8a5fa1064c6fc90a4274dcf733cbd87acbc10423619b8a676bd8e807c59cd7385817dabe10c042995cf1ddacc
+  metadata.gz: b98fa499807ee4488f8e38cc95b6f720567d137a7920c69eb741cd9d82fd550233b9554b4a1c09386fdfe11597fa695b12322560e3dbcad94bf42878b74d04eb
+  data.tar.gz: 984f7ed095292a2f7ef0fcf1dffad425c1cb48b72910f5cd683f0680909c544b4f560213937b33dc36056afeeae3fad8c9d62134e7a7e2f67274de755b6099cc

data/Gemfile

@@ -1,22 +1,19 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
-
-gem "activerecord",                    "~> 4.0.2"
-gem "activesupport",                   "~> 4.0.2"
-gem "mysql",                           "~> 2.9.1"
+gem "activerecord",                    "~> 4.2.9"
+gem "activesupport",                   "~> 4.2.9"
+gem "mysql2",                          "~> 0.4.9"
 gem "safe_attributes",                 "~> 1.0.10"
-gem "activerecord-deprecated_finders", "~> 1.0.3"
+gem "activerecord-deprecated_finders", "~> 1.0.4"
 gem "bio-genomic-interval",            ">= 0.1.2"
 
-
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rake",    ">= 10.1.0" 
+  gem "rake",    ">= 12.1.0" 
   gem "rspec",   ">= 2.14.1"
-  gem "bundler", ">= 1.3.5"
+  gem "bundler", ">= 1.15.4"
   gem "jeweler", ">= 2.3.7"
   gem "bio",     ">= 1.5.1"
   gem "rdoc",    ">= 4.0.1"
-  # gem "simplecov", :require => false, :group => :test
 end  

data/Gemfile.lock

@@ -1,26 +1,24 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activemodel (4.0.13)
-      activesupport (= 4.0.13)
-      builder (~> 3.1.0)
-    activerecord (4.0.13)
-      activemodel (= 4.0.13)
-      activerecord-deprecated_finders (~> 1.0.2)
-      activesupport (= 4.0.13)
-      arel (~> 4.0.0)
+    activemodel (4.2.9)
+      activesupport (= 4.2.9)
+      builder (~> 3.1)
+    activerecord (4.2.9)
+      activemodel (= 4.2.9)
+      activesupport (= 4.2.9)
+      arel (~> 6.0)
     activerecord-deprecated_finders (1.0.4)
-    activesupport (4.0.13)
-      i18n (~> 0.6, >= 0.6.9)
-      minitest (~> 4.2)
-      multi_json (~> 1.3)
-      thread_safe (~> 0.1)
-      tzinfo (~> 0.3.37)
+    activesupport (4.2.9)
+      i18n (~> 0.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.3, >= 0.3.4)
+      tzinfo (~> 1.1)
     addressable (2.4.0)
-    arel (4.0.2)
+    arel (6.0.4)
     bio (1.5.1)
     bio-genomic-interval (0.1.2)
-    builder (3.1.4)
+    builder (3.2.3)
     descendants_tracker (0.0.4)
       thread_safe (~> 0.3, >= 0.3.1)
     diff-lcs (1.3)
@@ -37,7 +35,6 @@ GEM
     hashie (3.5.6)
     highline (1.7.8)
     i18n (0.8.6)
-    jar-dependencies (0.3.11)
     jeweler (2.3.7)
       builder
       bundler (>= 1)
@@ -52,14 +49,13 @@ GEM
     jwt (1.5.6)
     mime-types (2.99.3)
     mini_portile2 (2.2.0)
-    minitest (4.7.5)
-    multi_json (1.12.1)
+    minitest (5.10.3)
+    multi_json (1.12.2)
     multi_xml (0.6.0)
     multipart-post (2.0.0)
-    mysql (2.9.1)
+    mysql2 (0.4.9)
     nokogiri (1.8.0)
       mini_portile2 (~> 2.2.0)
-    nokogiri (1.8.0-java)
     oauth2 (1.4.0)
       faraday (>= 0.8, < 0.13)
       jwt (~> 1.0)
@@ -67,10 +63,8 @@ GEM
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
     psych (2.2.4)
-    psych (2.2.4-java)
-      jar-dependencies (>= 0.1.7)
     rack (2.0.3)
-    rake (12.0.0)
+    rake (12.1.0)
     rdoc (5.1.0)
     rspec (3.6.0)
       rspec-core (~> 3.6.0)
@@ -89,26 +83,25 @@ GEM
       activerecord (>= 3.0.0)
     semver2 (3.4.2)
     thread_safe (0.3.6)
-    thread_safe (0.3.6-java)
-    tzinfo (0.3.53)
+    tzinfo (1.2.3)
+      thread_safe (~> 0.1)
 
 PLATFORMS
-  java
   ruby
 
 DEPENDENCIES
-  activerecord (~> 4.0.2)
-  activerecord-deprecated_finders (~> 1.0.3)
-  activesupport (~> 4.0.2)
+  activerecord (~> 4.2.9)
+  activerecord-deprecated_finders (~> 1.0.4)
+  activesupport (~> 4.2.9)
   bio (>= 1.5.1)
   bio-genomic-interval (>= 0.1.2)
-  bundler (>= 1.3.5)
+  bundler (>= 1.15.4)
   jeweler (>= 2.3.7)
-  mysql (~> 2.9.1)
-  rake (>= 10.1.0)
+  mysql2 (~> 0.4.9)
+  rake (>= 12.1.0)
   rdoc (>= 4.0.1)
   rspec (>= 2.14.1)
   safe_attributes (~> 1.0.10)
 
 BUNDLED WITH
-   1.14.2
+   1.15.4

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.6.3
+# bio-ucsc-api version 0.6.4
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -64,11 +64,11 @@ Supported Ruby interpreter implementations:
 
 Major rubygem dependencies:
 
-* active_record version **4.0** - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
+* active_record version **4.2** - http://api.rubyonrails.org/classes/ActiveRecord/Base.html
 * safe_attributes - https://github.com/bjones/safe_attributes
 * activerecord-deprecated_finders - http://github.com/rails/activerecord-deprecated_finders -- supporting AR4.0 deprecated dynamic finders shch as 'find_all_by_name'. To suppress deprecation warnings, you have to add `ActiveSupport::Deprecation.silenced = true`.
 * bioruby-genomic-interval - https://github.com/misshie/bioruby-genomic-interval
-* mysql (MySQL/Ruby MySQL API module) - http://www.tmtm.org/mysql/ruby/README.html
+* **mysql2** 0.4 https://github.com/brianmario/mysql2
 
 See also:
 
@@ -76,6 +76,7 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
+* **UPDATE** (v.0.6.4) Supporting Ruby 2.4 by using Rails 4.2 and the MySql2 gem v0.4 at BioHackathon2017 http://2017.biohackathon.org .
 * **BUG-FIX** (v.0.6.3) Bio::Ucsc::File::TwoBit#find_by_interval fails in retrieving reference sequences including entire "N" blocks, e.g. "aaaNNttt".
 * **BUG-FIX** (v.0.6.2) NoMemoryError in Bio::Ucsc::File::Twobit.open. Now internally File.open is used instead of Kernel.open.  
 * **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions. 

data/VERSION

@@ -1 +1 @@
-0.6.3
+0.6.4

data/bio-ucsc-api.gemspec

@@ -2,18 +2,18 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-ucsc-api 0.6.3 ruby lib
+# stub: bio-ucsc-api 0.6.4 ruby lib
 
 Gem::Specification.new do |s|
-  s.name = "bio-ucsc-api"
-  s.version = "0.6.3"
+  s.name = "bio-ucsc-api".freeze
+  s.version = "0.6.4"
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.require_paths = ["lib"]
-  s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
-  s.date = "2017-08-17"
-  s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
-  s.email = "missy@be.to"
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Hiroyuki Mishima".freeze, "Jan Aerts".freeze]
+  s.date = "2017-09-12"
+  s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby".freeze
+  s.email = "missy@be.to".freeze
   s.extra_rdoc_files = [
     "ChangeLog.md",
     "LICENSE.txt",
@@ -437,54 +437,54 @@ Gem::Specification.new do |s|
     "samples/snp2genes.rb",
     "samples/symbol2summary.rb"
   ]
-  s.homepage = "http://github.com/misshie/bioruby-ucsc-api"
-  s.licenses = ["The MIT License"]
-  s.rubygems_version = "2.5.1"
-  s.summary = "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
+  s.homepage = "http://github.com/misshie/bioruby-ucsc-api".freeze
+  s.licenses = ["The MIT License".freeze]
+  s.rubygems_version = "2.6.11".freeze
+  s.summary = "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby".freeze
 
   if s.respond_to? :specification_version then
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<activerecord>, ["~> 4.0.2"])
-      s.add_runtime_dependency(%q<activesupport>, ["~> 4.0.2"])
-      s.add_runtime_dependency(%q<mysql>, ["~> 2.9.1"])
-      s.add_runtime_dependency(%q<safe_attributes>, ["~> 1.0.10"])
-      s.add_runtime_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
-      s.add_runtime_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-      s.add_development_dependency(%q<rake>, [">= 10.1.0"])
-      s.add_development_dependency(%q<rspec>, [">= 2.14.1"])
-      s.add_development_dependency(%q<bundler>, [">= 1.3.5"])
-      s.add_development_dependency(%q<jeweler>, [">= 2.3.7"])
-      s.add_development_dependency(%q<bio>, [">= 1.5.1"])
-      s.add_development_dependency(%q<rdoc>, [">= 4.0.1"])
+      s.add_runtime_dependency(%q<activerecord>.freeze, ["~> 4.2.9"])
+      s.add_runtime_dependency(%q<activesupport>.freeze, ["~> 4.2.9"])
+      s.add_runtime_dependency(%q<mysql2>.freeze, ["~> 0.4.9"])
+      s.add_runtime_dependency(%q<safe_attributes>.freeze, ["~> 1.0.10"])
+      s.add_runtime_dependency(%q<activerecord-deprecated_finders>.freeze, ["~> 1.0.4"])
+      s.add_runtime_dependency(%q<bio-genomic-interval>.freeze, [">= 0.1.2"])
+      s.add_development_dependency(%q<rake>.freeze, [">= 12.1.0"])
+      s.add_development_dependency(%q<rspec>.freeze, [">= 2.14.1"])
+      s.add_development_dependency(%q<bundler>.freeze, [">= 1.15.4"])
+      s.add_development_dependency(%q<jeweler>.freeze, [">= 2.3.7"])
+      s.add_development_dependency(%q<bio>.freeze, [">= 1.5.1"])
+      s.add_development_dependency(%q<rdoc>.freeze, [">= 4.0.1"])
     else
-      s.add_dependency(%q<activerecord>, ["~> 4.0.2"])
-      s.add_dependency(%q<activesupport>, ["~> 4.0.2"])
-      s.add_dependency(%q<mysql>, ["~> 2.9.1"])
-      s.add_dependency(%q<safe_attributes>, ["~> 1.0.10"])
-      s.add_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
-      s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-      s.add_dependency(%q<rake>, [">= 10.1.0"])
-      s.add_dependency(%q<rspec>, [">= 2.14.1"])
-      s.add_dependency(%q<bundler>, [">= 1.3.5"])
-      s.add_dependency(%q<jeweler>, [">= 2.3.7"])
-      s.add_dependency(%q<bio>, [">= 1.5.1"])
-      s.add_dependency(%q<rdoc>, [">= 4.0.1"])
+      s.add_dependency(%q<activerecord>.freeze, ["~> 4.2.9"])
+      s.add_dependency(%q<activesupport>.freeze, ["~> 4.2.9"])
+      s.add_dependency(%q<mysql2>.freeze, ["~> 0.4.9"])
+      s.add_dependency(%q<safe_attributes>.freeze, ["~> 1.0.10"])
+      s.add_dependency(%q<activerecord-deprecated_finders>.freeze, ["~> 1.0.4"])
+      s.add_dependency(%q<bio-genomic-interval>.freeze, [">= 0.1.2"])
+      s.add_dependency(%q<rake>.freeze, [">= 12.1.0"])
+      s.add_dependency(%q<rspec>.freeze, [">= 2.14.1"])
+      s.add_dependency(%q<bundler>.freeze, [">= 1.15.4"])
+      s.add_dependency(%q<jeweler>.freeze, [">= 2.3.7"])
+      s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
+      s.add_dependency(%q<rdoc>.freeze, [">= 4.0.1"])
     end
   else
-    s.add_dependency(%q<activerecord>, ["~> 4.0.2"])
-    s.add_dependency(%q<activesupport>, ["~> 4.0.2"])
-    s.add_dependency(%q<mysql>, ["~> 2.9.1"])
-    s.add_dependency(%q<safe_attributes>, ["~> 1.0.10"])
-    s.add_dependency(%q<activerecord-deprecated_finders>, ["~> 1.0.3"])
-    s.add_dependency(%q<bio-genomic-interval>, [">= 0.1.2"])
-    s.add_dependency(%q<rake>, [">= 10.1.0"])
-    s.add_dependency(%q<rspec>, [">= 2.14.1"])
-    s.add_dependency(%q<bundler>, [">= 1.3.5"])
-    s.add_dependency(%q<jeweler>, [">= 2.3.7"])
-    s.add_dependency(%q<bio>, [">= 1.5.1"])
-    s.add_dependency(%q<rdoc>, [">= 4.0.1"])
+    s.add_dependency(%q<activerecord>.freeze, ["~> 4.2.9"])
+    s.add_dependency(%q<activesupport>.freeze, ["~> 4.2.9"])
+    s.add_dependency(%q<mysql2>.freeze, ["~> 0.4.9"])
+    s.add_dependency(%q<safe_attributes>.freeze, ["~> 1.0.10"])
+    s.add_dependency(%q<activerecord-deprecated_finders>.freeze, ["~> 1.0.4"])
+    s.add_dependency(%q<bio-genomic-interval>.freeze, [">= 0.1.2"])
+    s.add_dependency(%q<rake>.freeze, [">= 12.1.0"])
+    s.add_dependency(%q<rspec>.freeze, [">= 2.14.1"])
+    s.add_dependency(%q<bundler>.freeze, [">= 1.15.4"])
+    s.add_dependency(%q<jeweler>.freeze, [">= 2.3.7"])
+    s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
+    s.add_dependency(%q<rdoc>.freeze, [">= 4.0.1"])
   end
 end
 

data/lib/bio-ucsc.rb

@@ -7,11 +7,9 @@
 base = "#{::File.dirname(__FILE__)}/bio-ucsc"
 
 require 'rubygems'
-gem 'activerecord', "~> 4.0.2"
+require "active_support"
 require "active_record"
-gem "safe_attributes"
 require "safe_attributes"
-gem "activerecord-deprecated_finders"
 require "active_record/deprecated_finders"
 #ActiveSupport::Deprecation.silenced = true
 
@@ -21,7 +19,7 @@ require "#{base}/gi.rb"
 
 module Bio
   module Ucsc
-    VERSION = "0.6.3"
+    VERSION = "0.6.4"
     base = "#{::File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################

data/lib/bio-ucsc/ailmel1.rb

@@ -1,9 +1,9 @@
 #
 # = AUTOMATIC Table Definition of the Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011-2017
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
+# License::     The MIT licence
 #
 
 require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -30,7 +30,7 @@ module Bio
         include SafeAttributes
         self.inheritance_column = 'dummy_not_to_use'
 
-        @@db_adapter  ||= 'mysql'
+        @@db_adapter  ||= 'mysql2'
         @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
         @@db_username ||= 'genome'
         @@db_password ||= ''
@@ -41,7 +41,7 @@ module Bio
         self.abstract_class = true
 
         def self.default
-          @@db_adapter  = 'mysql'
+          @@db_adapter  = 'mysql2'
           @@db_host     = 'genome-mysql.cse.ucsc.edu'
           @@db_username = 'genome'
           @@db_password = ''

data/lib/bio-ucsc/anocar2.rb

@@ -1,9 +1,9 @@
 #
 # = AUTOMATIC Table Definition of the Lizard May 2010 (Broad AnoCar2.0/anoCar2) assembly
-# Copyright::   Copyright (C) 2011, 2012
+# Copyright::   Copyright (C) 2011-2017
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
+# License::     The MIT licence
 #
 
 require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -30,7 +30,7 @@ module Bio
         include SafeAttributes
         self.inheritance_column = 'dummy_not_to_use'
 
-        @@db_adapter  ||= 'mysql'
+        @@db_adapter  ||= 'mysql2'
         @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
         @@db_username ||= 'genome'
         @@db_password ||= ''
@@ -41,7 +41,7 @@ module Bio
         self.abstract_class = true
 
         def self.default
-          @@db_adapter  = 'mysql'
+          @@db_adapter  = 'mysql2'
           @@db_host     = 'genome-mysql.cse.ucsc.edu'
           @@db_username = 'genome'
           @@db_password = ''

data/lib/bio-ucsc/anogam1.rb

@@ -1,9 +1,9 @@
 #
 # = AUTOMATIC Table Definition of the A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) assembly
-# Copyright::   Copyright (C) 2011, 2012
+# Copyright::   Copyright (C) 2011-2017
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
+# License::     The MIT licence
 #
 
 require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -30,7 +30,7 @@ module Bio
         include SafeAttributes
         self.inheritance_column = 'dummy_not_to_use'
 
-        @@db_adapter  ||= 'mysql'
+        @@db_adapter  ||= 'mysql2'
         @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
         @@db_username ||= 'genome'
         @@db_password ||= ''
@@ -41,7 +41,7 @@ module Bio
         self.abstract_class = true
 
         def self.default
-          @@db_adapter  = 'mysql'
+          @@db_adapter  = 'mysql2'
           @@db_host     = 'genome-mysql.cse.ucsc.edu'
           @@db_username = 'genome'
           @@db_password = ''

data/lib/bio-ucsc/apimel2.rb

@@ -1,9 +1,9 @@
 #
 # = AUTOMATIC Table Definition of the A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011-2017
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
+# License::     The MIT licence
 #
 
 require "#{::File.dirname(__FILE__)}/table_class_detector"
@@ -32,7 +32,7 @@ Group11 Group12 Group13 Group14 Group15 Group16 GroupUn)
         include SafeAttributes
         self.inheritance_column = 'dummy_not_to_use'
 
-        @@db_adapter  ||= 'mysql'
+        @@db_adapter  ||= 'mysql2'
         @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
         @@db_username ||= 'genome'
         @@db_password ||= ''
@@ -43,7 +43,7 @@ Group11 Group12 Group13 Group14 Group15 Group16 GroupUn)
         self.abstract_class = true
 
         def self.default
-          @@db_adapter  = 'mysql'
+          @@db_adapter  = 'mysql2'
           @@db_host     = 'genome-mysql.cse.ucsc.edu'
           @@db_username = 'genome'
           @@db_password = ''