bio 1.5.0 → 1.5.1

data/RELEASE_NOTES.rdoc

@@ -1,3 +1,29 @@
+= BioRuby 1.5.1 RELEASE NOTES
+
+Few changes have been made to the BioRuby 1.5.1 after the version 1.5.0 is
+released.
+
+== NEWS
+
+=== HTTPS is used to access NCBI web services
+
+As you may know, NCBI announced that all HTTP resources will be switched
+to HTTPS on September 30, 2016. To follow the transition, all URLs for
+accessing NCBI E-utilities in BioRuby are changed to use HTTPS.
+
+In BioRuby, the following classes/modules are affected.
+
+* Bio::NCBI::REST and descending classes
+* Bio::PubMed
+
+In some rare cases (especially when building Ruby and/or OpenSSL by yourself
+from source code), Ruby does not include SSL/TLS support, or Ruby fails to
+detect SSL root certificates. In such cases, you may need to reinstall or
+upgrade Ruby, OpenSSL (or alternatives), and/or SSL root certificates with
+appropriate configuration options. Alternatively, installing binary packages
+is generally a good idea.
+
+
 = BioRuby 1.5.0 RELEASE NOTES
 
 A lot of changes have been made to the BioRuby 1.5.0 after the version 1.4.3
@@ -21,7 +47,7 @@ This release is the final BioRuby version that can be run on Ruby 1.8.
 
 BioRuby is distributed under the same license as Ruby's. In October 2011,
 Ruby's License was changed from a dual license with GPLv2 to a dual license
-with 2-clause BSDL.available. Since BioRuby 1.5.0, we have updated to the
+with 2-clause BSDL. Since BioRuby 1.5.0, we have updated to the
 new version of Ruby's License. For details about the license, see COPYING
 or COPYING.ja and BSDL. In addition, please do not forget to see LEGAL for
 exception files that are subjected to different licenses.
@@ -29,7 +55,7 @@ exception files that are subjected to different licenses.
 === Semantic Versioning will be introduced
 
 We will adopt the Semantic Versioning since the next release version, which
-will be BioRuby 1.5.1. This means that BioRuby 1.5.0 are NOT subject to the
+will be BioRuby 1.5.1. This means that BioRuby 1.5.0 is NOT subject to the
 Semantic Versioning.
 
 

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.5.0"
+  s.version = "1.5.1"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"

data/lib/bio/command.rb

@@ -13,6 +13,7 @@ require 'uri'
 require 'open-uri'
 require 'cgi'
 require 'net/http'
+require 'net/https'
 require 'tmpdir'
 require 'fileutils'
 
@@ -706,6 +707,43 @@ module Command
     OpenURI.open_uri(uri).read
   end
 
+  # Same as:
+  #   Net::HTTP.start(uri.address, uri.port)
+  # and
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  # It supports https.
+  #
+  # Note: This method ignores uri.path.
+  # It only uses uri.address and uri.port.
+  #
+  # ---
+  # *Arguments*:
+  # * (required) _uri_: URI object or String containing URI
+  # *Returns*:: (same as Net::HTTP::start except for proxy and https support)
+  def start_http_uri(uri, &block)
+    unless uri.is_a?(URI)
+      uri = URI.parse(uri)
+    end
+
+    # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
+    # If the spec of open-uri.rb would be changed, we should change below.
+    if proxyuri = uri.find_proxy then
+      raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
+      klass = Net::HTTP.Proxy(proxyuri.host, proxyuri.port)
+    else
+      klass = Net::HTTP
+    end
+
+    http = klass.new(uri.host, uri.port)
+    case uri.scheme
+    when 'https'
+      http.use_ssl = true
+    end
+
+    http.start(&block)
+  end
+
   # Same as:
   #   Net::HTTP.start(address, port)
   # and 
@@ -813,7 +851,7 @@ module Command
     }
     hash.update(header)
 
-    start_http(uri.host, uri.port) do |http|
+    start_http_uri(uri) do |http|
       http.post(uri.path, data, hash)
     end
   end
@@ -937,7 +975,7 @@ module Command
     }
     hash.update(header)
 
-    start_http(uri.host, uri.port) do |http|
+    start_http_uri(uri) do |http|
       http.post(uri.path, data, hash)
     end
   end

data/lib/bio/io/ncbirest.rb

@@ -20,13 +20,13 @@ class NCBI
   # They may also be used for other NCBI services.
   ENTREZ_DEFAULT_PARAMETERS = {
     # Cited from
-    # http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.Release_Notes
+    # https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.Release_Notes
     #  tool:
     #  Name of application making the E-utility call.
     #  Value must be a string with no internal spaces.
     'tool' => "bioruby",
     # Cited from
-    # http://www.ncbi.nlm.nih.gov/books/NBK25497/
+    # https://www.ncbi.nlm.nih.gov/books/NBK25497/
     # The value of email should be a complete and valid e-mail address
     # of the software developer and not that of a third-party end user.
     'email' => 'staff@bioruby.org',
@@ -54,7 +54,7 @@ class NCBI
   # Sets default email address used for Entrez (eUtils).
   # It may also be used for other NCBI services.
   #
-  # In http://www.ncbi.nlm.nih.gov/books/NBK25497/ 
+  # In https://www.ncbi.nlm.nih.gov/books/NBK25497/ 
   # NCBI says:
   # "The value of email should be a complete and valid e-mail address of
   # the software developer and not that of a third-party end user."
@@ -89,7 +89,7 @@ class NCBI
   # Sets default tool name for Entrez (eUtils).
   # It may also be used for other NCBI services.
   #
-  # In http://www.ncbi.nlm.nih.gov/books/NBK25497/ 
+  # In https://www.ncbi.nlm.nih.gov/books/NBK25497/ 
   # NCBI says:
   # "The value of tool should be a string with no internal spaces that
   # uniquely identifies the software producing the request."
@@ -111,9 +111,10 @@ class NCBI
 #
 # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
 #
-# Entrez utilities index:
+# Entrez Programming Utilities Help:
 #
-# * http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
+# * https://www.ncbi.nlm.nih.gov/books/NBK25501/
+# * ( redirected from http://www.ncbi.nlm.nih.gov/entrez/utils/ )
 #
 class REST
 
@@ -197,7 +198,7 @@ class REST
 
   # List the NCBI database names E-Utils (einfo) service
   # 
-  # * http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
+  # * https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
   #
   #  pubmed protein nucleotide nuccore nucgss nucest structure genome
   #  books cancerchromosomes cdd gap domains gene genomeprj gensat geo
@@ -215,7 +216,7 @@ class REST
   # ---
   # *Returns*:: array of string (database names)
   def einfo
-    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"
+    serv = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"
     opts = default_parameters.merge({})
     response = ncbi_post_form(serv, opts)
     result = response.body
@@ -229,8 +230,9 @@ class REST
   # 
   # For information on the possible arguments, see
   #
-  # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
-  # * http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip
+  # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
+  # * ( redirected from http://eutils.ncbi.nlm.nih.gov/books/n/helpeutils/chapter4/#chapter4.ESearch )
+  # * ( redirected from http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html )
   #
   # == Usage
   #
@@ -282,7 +284,7 @@ class REST
   # * _step_: maximum number of entries retrieved at a time
   # *Returns*:: array of entry IDs or a number of results
   def esearch(str, hash = {}, limit = nil, step = 10000)
-    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+    serv = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
     opts = default_parameters.merge({ "term" => str })
     opts.update(hash)
 
@@ -313,7 +315,7 @@ class REST
   # *Arguments*:: same as esearch method
   # *Returns*:: array of entry IDs or a number of results
   def esearch_count(str, hash = {})
-    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+    serv = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
     opts = default_parameters.merge({ "term" => str })
     opts.update(hash)
     opts.update("rettype" => "count")
@@ -328,7 +330,7 @@ class REST
   #
   # For information on the possible arguments, see
   #
-  # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
+  # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
   #
   # == Usage
   #
@@ -351,7 +353,7 @@ class REST
   # * _step_: maximum number of entries retrieved at a time
   # *Returns*:: String
   def efetch(ids, hash = {}, step = 100)
-    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
+    serv = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
     opts = default_parameters.merge({ "retmode"  => "text" })
     opts.update(hash)
 
@@ -396,12 +398,12 @@ class REST
 
     # Search database entries by given keywords using E-Utils (esearch).
     #
-    # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
+    # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
     #
     #  sequences = gene + genome + nucleotide + protein + popset + snp
     #  nucleotide = nuccore + nucest + nucgss
     #
-    # * http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
+    # * https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
     #
     #  pubmed protein nucleotide nuccore nucgss nucest structure genome
     #  books cancerchromosomes cdd gap domains gene genomeprj gensat geo
@@ -517,7 +519,7 @@ class REST
 
       # Retrieve sequence entries by given IDs using E-Utils (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #
       #  sequences = gene + genome + nucleotide + protein + popset + snp
       #  nucleotide = nuccore + nucest + nucgss
@@ -581,7 +583,7 @@ class REST
       # Retrieve nucleotide sequence entries by given IDs using E-Utils
       # (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #  nucleotide = nuccore + nucest + nucgss
       #
       # format (rettype):
@@ -643,7 +645,7 @@ class REST
       # Retrieve protein sequence entries by given IDs using E-Utils
       # (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #  protein
       #
       # format (rettype):
@@ -699,7 +701,7 @@ class REST
 
       # Retrieve PubMed entries by given IDs using E-Utils (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #
       # == Usage
       #
@@ -741,7 +743,7 @@ class REST
 
       # Retrieve PubMed Central entries by given IDs using E-Utils (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #
       # == Usage
       #
@@ -776,7 +778,7 @@ class REST
 
       # Retrieve journal entries by given IDs using E-Utils (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #
       # == Usage
       #
@@ -811,7 +813,7 @@ class REST
 
       # Retrieve OMIM entries by given IDs using E-Utils (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #
       # == Usage
       #
@@ -849,7 +851,7 @@ class REST
 
       # Retrieve taxonomy entries by given IDs using E-Utils (efetch).
       #
-      # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchtax_help.html
+      # * https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
       #
       # == Usage
       #

data/lib/bio/version.rb

@@ -10,7 +10,7 @@
 module Bio
 
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 5, 0].extend(Comparable).freeze
+  BIORUBY_VERSION = [1, 5, 1].extend(Comparable).freeze
 
   # Extra version specifier (String or nil).
   # Existance of the value indicates development version.
@@ -22,7 +22,7 @@ module Bio
   # By default, if the third digit (teeny) of BIORUBY_VERSION is 0,
   # the version is regarded as a development version.
   BIORUBY_EXTRA_VERSION =
-    nil #(BIORUBY_VERSION[2] == 0) ? "-dev" : nil
+    nil #"-dev" #(BIORUBY_VERSION[2] == 0) ? "-dev" : nil
 
   # Version identifier, including extra version string (String)
   # Unlike BIORUBY_VERSION, it is not comparable.

data/test/network/bio/test_command.rb

@@ -13,6 +13,7 @@ load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
 
 # libraries needed for the tests
 require 'test/unit'
+require 'uri'
 require 'bio/command'
 
 module Bio
@@ -22,6 +23,7 @@ module Bio
       @port = 80 
       @path = "/"
       @url = "http://bioruby.open-bio.org:80/"
+      @uri = URI.parse(@url)
     end
 
     def test_read_uri
@@ -32,6 +34,21 @@ module Bio
       assert(!str.to_s.empty?)
     end
 
+    def test_start_http_uri
+      ht = Bio::Command.start_http_uri(@uri)
+      assert_kind_of(Net::HTTP, ht)
+      res = ht.get(@path)
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
+    def test_start_http_uri_with_block
+      res = Bio::Command.start_http_uri(@uri) do |ht|
+        assert_kind_of(Net::HTTP, ht)
+        ht.get(@path)
+      end
+      assert_kind_of(Net::HTTPResponse, res)
+    end
+
     def test_start_http
       ht = Bio::Command.start_http(@host, @port)
       assert_kind_of(Net::HTTP, ht)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio
 version: !ruby/object:Gem::Version
-  version: 1.5.0
+  version: 1.5.1
 platform: ruby
 authors:
 - BioRuby project
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-01 00:00:00.000000000 Z
+date: 2016-09-07 00:00:00.000000000 Z
 dependencies: []
 description: BioRuby is a library for bioinformatics (biology + information science).
 email: staff@bioruby.org
@@ -674,7 +674,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Bioinformatics library