bio 1.6.0.pre.20181210 → 2.0.0

data/appveyor.yml

@@ -6,16 +6,24 @@ branches:
 clone_depth: 10
 install:
   - SET PATH=C:\Ruby%ruby_version%\bin;%PATH%
+  - SET BUNDLE_GEMFILE=gemfiles/Gemfile.windows
+  - bundle install
+  - bundle exec rake regemspec
+  - bundle exec rake gem
+  - bundle exec gem install pkg/bio-*.gem
+  - echo gem "bio" >> gemfiles\Gemfile.windows
+build: off
+before_test:
   - ruby --version
   - gem --version
-  - gem build bioruby.gemspec
-  - gem install *.gem
-build: off
+  - bundle --version
+test_script:
+  - bundle exec rake gem-test
 environment:
   matrix:
-    - ruby_version: "21"
-    - ruby_version: "21-x64"
-    - ruby_version: "22"
-    - ruby_version: "22-x64"
     - ruby_version: "23"
     - ruby_version: "23-x64"
+    - ruby_version: "24"
+    - ruby_version: "24-x64"
+    - ruby_version: "25"
+    - ruby_version: "25-x64"

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.6.0.pre.20181211"
+  s.version = "2.0.0"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -54,6 +54,7 @@ Gem::Specification.new do |s|
     "gemfiles/Gemfile.travis-rbx",
     "gemfiles/Gemfile.travis-ruby1.8",
     "gemfiles/Gemfile.travis-ruby1.9",
+    "gemfiles/Gemfile.windows",
     "gemfiles/modify-Gemfile.rb",
     "gemfiles/prepare-gemspec.rb",
     "lib/bio.rb",
@@ -69,7 +70,6 @@ Gem::Specification.new do |s|
     "lib/bio/appl/blast/rexml.rb",
     "lib/bio/appl/blast/rpsblast.rb",
     "lib/bio/appl/blast/wublast.rb",
-    "lib/bio/appl/blast/xmlparser.rb",
     "lib/bio/appl/blat/report.rb",
     "lib/bio/appl/clustalw.rb",
     "lib/bio/appl/clustalw/report.rb",
@@ -316,7 +316,6 @@ Gem::Specification.new do |s|
     "sample/test_restriction_enzyme_long.rb",
     "sample/tfastx2tab.rb",
     "sample/vs-genes.rb",
-    "setup.rb",
     "test/bioruby_test_helper.rb",
     "test/data/HMMER/hmmpfam.out",
     "test/data/HMMER/hmmsearch.out",
@@ -452,6 +451,7 @@ Gem::Specification.new do |s|
     "test/network/bio/appl/blast/test_remote.rb",
     "test/network/bio/appl/test_blast.rb",
     "test/network/bio/appl/test_pts1.rb",
+    "test/network/bio/db/kegg/test_genes_hsa7422.rb",
     "test/network/bio/io/test_pubmed.rb",
     "test/network/bio/io/test_togows.rb",
     "test/network/bio/test_command.rb",

data/gemfiles/Gemfile.travis-rbx

@@ -3,8 +3,6 @@ source "https://rubygems.org"
 gem "rake"
 gem "rdoc"
 
-gem "xmlparser"
-
 platforms :rbx do
   gem 'racc'
   gem 'rubysl', '~> 2.0'

data/gemfiles/Gemfile.travis-ruby1.8

@@ -4,5 +4,3 @@ gem "rake", "~>10.4"
 # rdoc 4.3.0 requires Ruby >= 1.9.3
 gem "rdoc", "~>4.2.0"
 
-gem "xmlparser", "~>0.7.2"
-

data/gemfiles/Gemfile.travis-ruby1.9

@@ -3,5 +3,3 @@ source "https://rubygems.org"
 gem "rake"
 gem "rdoc"
 
-gem "xmlparser"
-

data/gemfiles/Gemfile.windows

@@ -0,0 +1,6 @@
+source "https://rubygems.org"
+
+gem "rake"
+gem "rdoc"
+gem "test-unit"
+

data/lib/bio/appl/blast/report.rb

@@ -43,18 +43,20 @@ class Report
   #--
   # require lines moved here to avoid circular require
   #++
-  require 'bio/appl/blast/xmlparser'
   require 'bio/appl/blast/rexml'
   require 'bio/appl/blast/format8'
 
+  #--
+  # loading bio-blast-xmlparser plugin if available
+  #++
+  begin
+    require 'bio-blast-xmlparser'
+  rescue LoadError
+  end
+
   # for Bio::FlatFile support (only for XML data)
   DELIMITER = RS = "</BlastOutput>\n"
 
-  # Specify to use XMLParser to parse XML (-m 7) output.
-  def self.xmlparser(data)
-    self.new(data, :xmlparser)
-  end
-
   # Specify to use REXML to parse XML (-m 7) output.
   def self.rexml(data)
     self.new(data, :rexml)
@@ -67,7 +69,7 @@ class Report
 
   def auto_parse(data)
     if /<?xml/.match(data[/.*/])
-      if defined?(XMLParser)
+      if defined? xmlparser_parse
         xmlparser_parse(data)
         @reports = blastxml_split_reports
       else
@@ -87,7 +89,11 @@ class Report
     @parameters = {}
     case parser
     when :xmlparser		# format 7
-      xmlparser_parse(data)
+      if defined? xmlparser_parse
+        xmlparser_parse(data)
+      else
+        raise NameError, "xmlparser_parse does not defined"
+      end
       @reports = blastxml_split_reports
     when :rexml		# format 7
       rexml_parse(data)
@@ -383,6 +389,32 @@ class Report
   attr_reader :reports
  
   private
+  # set parameter of the key as val
+  def xml_set_parameter(key, val)
+    #labels = { 
+    #  'matrix'       => 'Parameters_matrix',
+    #  'expect'       => 'Parameters_expect',
+    #  'include'      => 'Parameters_include',
+    #  'sc-match'     => 'Parameters_sc-match',
+    #  'sc-mismatch'  => 'Parameters_sc-mismatch',
+    #  'gap-open'     => 'Parameters_gap-open',
+    #  'gap-extend'   => 'Parameters_gap-extend',
+    #  'filter'       => 'Parameters_filter',
+    #  'pattern'      => 'Parameters_pattern',
+    #  'entrez-query' => 'Parameters_entrez-query',
+    #}
+    k = key.sub(/\AParameters\_/, '')
+    @parameters[k] =
+      case k
+      when 'expect', 'include'
+        val.to_f
+      when /\Agap\-/, /\Asc\-/
+        val.to_i
+      else
+        val
+      end
+  end
+
   # (private method)
   # In new BLAST XML (blastall >= 2.2.14), results of multiple queries
   # are stored in <Iteration>. This method splits iterations into

data/lib/bio/db/kegg/common.rb

@@ -210,6 +210,20 @@ class KEGG
       private :strings_as_hash
     end #module StringsAsHash
 
+    # This module provides diseases_as_hash method.
+    #
+    # Bio::KEGG::* internal use only.
+    module DiseasesAsHash 
+      include StringsAsHash
+      # Returns a Hash of the disease ID and its definition
+      def diseases_as_hash
+        unless (defined? @diseases_as_hash) && @diseases_as_hash
+          @diseases_as_hash = strings_as_hash(diseases_as_strings)
+        end
+        @diseases_as_hash
+      end
+    end #module DiseasesAsHash
+
   end #module Common
 end #class KEGG
 end #module Bio

data/lib/bio/db/kegg/genes.rb

@@ -107,6 +107,11 @@ class GENES < KEGGDB
   def orthologs_as_hash; super; end if false #dummy for RDoc
   alias orthologs orthologs_as_hash
 
+  include Common::DiseasesAsHash
+  # Returns a Hash of the disease ID and its definition
+  def diseases_as_hash; super; end if false #dummy for RDoc
+  alias diseases diseases_as_hash
+
   # Creates a new Bio::KEGG::GENES object.
   # ---
   # *Arguments*:
@@ -238,6 +243,27 @@ class GENES < KEGGDB
     lines_fetch('PATHWAY')
   end
 
+  # Networks described in the NETWORK lines.
+  # ---
+  # *Returns*:: Array containing String
+  def networks_as_strings
+    lines_fetch('NETWORK')
+  end
+
+  # Diseases described in the DISEASE lines.
+  # ---
+  # *Returns*:: Array containing String
+  def diseases_as_strings
+    lines_fetch('DISEASE')
+  end
+  
+  # Drug targets described in the DRUG_TARGET lines.
+  # ---
+  # *Returns*:: Array containing String
+  def drug_targets_as_strings
+    lines_fetch('DRUG_TARGET')
+  end
+
   # Returns CLASS field of the entry.
   def keggclass
     field_fetch('CLASS')

data/lib/bio/db/kegg/pathway.rb

@@ -42,6 +42,11 @@ class PATHWAY < KEGGDB
   def orthologs_as_hash; super; end if false #dummy for RDoc
   alias orthologs orthologs_as_hash
 
+  include Common::DiseasesAsHash
+  # Returns a Hash of the disease ID and its definition
+  def diseases_as_hash; super; end if false #dummy for RDoc
+  alias diseases diseases_as_hash
+
   include Common::References
   # REFERENCE -- Returns contents of the REFERENCE records as an Array of
   # Bio::Reference objects.
@@ -122,17 +127,6 @@ class PATHWAY < KEGGDB
     lines_fetch('DISEASE')
   end
 
-  # Diseases described in the DISEASE lines.
-  # ---
-  # *Returns*:: Hash of disease ID and its definition
-  def diseases_as_hash
-    unless (defined? @diseases_as_hash) && @diseases_as_hash
-      @diseases_as_hash = strings_as_hash(diseases_as_strings)
-    end
-    @diseases_as_hash
-  end
-  alias diseases diseases_as_hash
-
   # Returns an Array of a database name and entry IDs in DBLINKS field.
   # ---
   # *Returns*:: Array containing String

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 6, 0].extend(Comparable).freeze
+  BIORUBY_VERSION = [2, 0, 0].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.
@@ -19,8 +19,8 @@ module Bio
   # ".pre           :: Pre-release version.
   #
   # References: https://guides.rubygems.org/patterns/#prerelease-gems
-  BIORUBY_EXTRA_VERSION = #nil
-    ".pre"
+  BIORUBY_EXTRA_VERSION = nil
+    #".pre"
 
   # Version identifier, including extra version string (String)
   # Unlike BIORUBY_VERSION, it is not comparable.

data/test/network/bio/db/kegg/test_genes_hsa7422.rb

@@ -0,0 +1,91 @@
+#
+# test/network/bio/db/kegg/test_genes_hsa7422.rb - Unit test for Bio::KEGG::GENES
+#
+# Copyright::  Copyright (C) 2019 BioRuby Project <staff@bioruby.org>
+# License::    The Ruby License
+# Contributor:: kojix2 <2xijok@gmail.com>
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/kegg/genes'
+require 'bio/io/togows'
+
+module Bio
+
+  # This test is moved from test/unit/bio/db/kegg/test_genes.rb
+  # and modified to get sample data from the internet
+  # because of KEGG data license issue.
+  #
+  # Note that this test may fail due to the data entry updates in KEGG.
+  class TestBioKEGGGENES_hsa7422 < Test::Unit::TestCase
+
+    str = Bio::TogoWS::REST.entry("kegg-genes", "hsa:7422")
+    DATA = str.freeze
+
+    def setup
+      #filename = File.join(BioRubyTestDataPath, 'KEGG/hsa7422.gene')
+      @obj = Bio::KEGG::GENES.new(DATA)
+    end
+
+    def test_diseases_as_strings
+      expected = ["H01456  Diabetic nephropathy",
+                  "H01457  Diabetic retinopathy",
+                  "H01459  Diabetic neuropathy",
+                  "H01529  Avascular necrosis of femoral head",
+                  "H01709  Glucocorticoid-induced osteonecrosis"]
+
+      assert_equal(expected, @obj.diseases_as_strings)
+    end
+
+    def test_diseases_as_hash
+      expected = {"H01456"=>"Diabetic nephropathy",
+                  "H01457"=>"Diabetic retinopathy",
+                  "H01459"=>"Diabetic neuropathy",
+                  "H01529"=>"Avascular necrosis of femoral head",
+                  "H01709"=>"Glucocorticoid-induced osteonecrosis"}
+      assert_equal(expected, @obj.diseases_as_hash)
+    end
+
+    def test_drug_targets_as_strings
+      expected = ["Abicipar pegol: D11517",
+                  "Aflibercept: D09574",
+                  "Aflibercept beta: D10819",
+                  "Bevacizumab: D06409",
+                  "Bevasiranib sodium: D08874",
+                  "Brolucizumab: D11083",
+                  "Faricimab: D11516",
+                  "Navicixizumab: D11126",
+                  "Pegaptanib: D05386",
+                  "Ranibizumab: D05697",
+                  "Vanucizumab: D11244"]
+      assert_equal(expected, @obj.drug_targets_as_strings)
+    end
+
+    def test_networks_as_strings
+      expected = ["nt06114  PI3K signaling (virus)",
+                  "nt06124  Chemokine signaling (virus)",
+                  "nt06164  Kaposi sarcoma-associated herpesvirus (KSHV)",
+                  "nt06214  PI3K signaling",
+                  "nt06219  JAK-STAT signaling",
+                  "nt06224  CXCR signaling",
+                  "nt06225  HIF-1 signaling",
+                  "nt06262  Pancreatic cancer",
+                  "nt06264  Renal cell carcinoma",
+                  "N00079  HIF-1 signaling pathway",
+                  "N00080  Loss of VHL to HIF-1 signaling pathway",
+                  "N00081  Mutation-inactivated VHL to HIF-1 signaling pathway",
+                  "N00095  ERBB2-overexpression to EGF-Jak-STAT signaling pathway",
+                  "N00157  KSHV vGPCR to GNB/G-ERK signaling pathway",
+                  "N00179  KSHV K1 to PI3K-NFKB signaling pathway"]
+      assert_equal(expected, @obj.networks_as_strings)
+    end
+
+  end #class TestBioKEGGGENES_hsa7422
+
+end #module Bio

data/test/unit/bio/appl/blast/test_report.rb

@@ -479,7 +479,7 @@ module Bio
     include TemplateTestBlastReportHsp
   end
 
-  if defined? XMLParser then
+  if Bio::Blast::Report.private_method_defined? :xmlparser_parse then
 
   class TestBlastReportXMLParser < Test::Unit::TestCase
     include TemplateTestBlastReport
@@ -497,7 +497,7 @@ module Bio
     include TemplateTestBlastReportHsp
   end
 
-  end #if defined? XMLParser
+  end #if
 
   class TestBlastReportDefault < Test::Unit::TestCase
     include TemplateTestBlastReport
@@ -1294,7 +1294,7 @@ module Bio
   end
 
   # Tests for XMLParser version
-  if defined? XMLParser then
+  if Bio::Blast::Report.private_method_defined? :xmlparser_parse then
 
   class TestBlastReportMultiXMLParser < Test::Unit::TestCase
     include TemplateTestBlastReportMulti
@@ -1312,6 +1312,6 @@ module Bio
     include TemplateTestBlastReportHspMulti
   end
 
-  end #if defined? XMLParser
+  end #if
 
 end # module Bio

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 1.6.0.pre.20181210
+  version: 2.0.0
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-11 00:00:00.000000000 Z
+date: 2019-06-14 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
@@ -65,6 +65,7 @@ files:
 - gemfiles/Gemfile.travis-rbx
 - gemfiles/Gemfile.travis-ruby1.8
 - gemfiles/Gemfile.travis-ruby1.9
+- gemfiles/Gemfile.windows
 - gemfiles/modify-Gemfile.rb
 - gemfiles/prepare-gemspec.rb
 - lib/bio.rb
@@ -80,7 +81,6 @@ files:
 - lib/bio/appl/blast/rexml.rb
 - lib/bio/appl/blast/rpsblast.rb
 - lib/bio/appl/blast/wublast.rb
-- lib/bio/appl/blast/xmlparser.rb
 - lib/bio/appl/blat/report.rb
 - lib/bio/appl/clustalw.rb
 - lib/bio/appl/clustalw/report.rb
@@ -327,7 +327,6 @@ files:
 - sample/test_restriction_enzyme_long.rb
 - sample/tfastx2tab.rb
 - sample/vs-genes.rb
-- setup.rb
 - test/bioruby_test_helper.rb
 - test/data/HMMER/hmmpfam.out
 - test/data/HMMER/hmmsearch.out
@@ -463,6 +462,7 @@ files:
 - test/network/bio/appl/blast/test_remote.rb
 - test/network/bio/appl/test_blast.rb
 - test/network/bio/appl/test_pts1.rb
+- test/network/bio/db/kegg/test_genes_hsa7422.rb
 - test/network/bio/io/test_pubmed.rb
 - test/network/bio/io/test_togows.rb
 - test/network/bio/test_command.rb
@@ -603,12 +603,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.6
+rubygems_version: 2.7.6.2
 signing_key: 
 specification_version: 4
 summary: Bioinformatics library